In the 9-qubit Shor code, the stabilizer S is generated by the following operators
\begin{align*} S_1=& Z_1Z_2 \\ S_2=&Z_2Z_3 \\ S_3=&Z_4Z_5 \\ S_4=&Z_5Z_6 \\ S_5=&Z_7Z_8 \\ S_6=&Z_8Z_9 \\ S_7=&X_1X_2X_3X_4X_5X_6 \\ S_8=&X_4X_5X_6X_7X_8X_9. \\ \end{align*}
Thus, the the dimension of the code space is 2^{9-8}=2, which implies that the code only encodes one logical qubit. In this case, \hat{N}(S)/S\cong \hat{P}_1, so \hat{N}/S will be generated by some elements \overline{X}, \overline{Z}\in\hat{N}(S)\backslash S, satisfying the usual Pauli commutation relations:
\overline{X}^2=\overline{Z}^2=\overline{I}, \ \text{and} \ \overline{X} \ \overline{Z}=-\overline{Z} \ \overline{X}
In this regard, let
\begin{align*} \overline{Z}=&X_1X_2X_3X_4X_5X_6X_7X_8X_9 \\ \overline{X}=& Z_1Z_2Z_3Z_4Z_5Z_6Z_7Z_8Z_9 \\ \end{align*}
which satisfy the commutation relations described above. Moreover, \overline{Z}\in\hat{N}(S)\backslash S. To see this, note that
\begin{align*} [\overline{Z},S_i]=0&, \ \text{for} \ i=7,8 \\ [\overline{X},S_i]=0&, \ \text{for} \ i=1,2,3,4,5,6 \\ \end{align*}
because each of these ease either a product of only X operators or only Z operators. The less trivial relations
\begin{align*} [\overline{Z},S_i]=0&, \ \text{for} \ i=1,2,3,4,5,6 \\ [\overline{X},S_i]=0&, \ \text{for} \ i=7,8 \\ \end{align*}
also hold, because the intersection of the supports of \overline{Z} and S_i ( for i=1,2,3,4,5,6 ) is always an even number of qubits. Likewise, the intersection of the supports of \overline{X} and S_i ( for i=7,8 ) is also always an even number of qubits. Thus, \overline{X},\overline{Z}\in \hat{N}(S).
Now, to see that \overline{X},\overline{Z}\notin S observe that the productS_7S_8=X_1X_2X_3X_7X_8X_9\neq\overline{Z}, which implies \overline{Z}\notin S. For \overline{X}, it is impossible to even generate an operator that contains all the factors Z_1Z_2Z_3 since the only stabilizers that even have nontrivial support on these first three qubits are S_1 and S_2, but yet S_1S_2=Z_1Z_3\neq Z_1Z_2Z_3. Therefore, \overline{X}\notin S.
Consider the binary matrix
\delta=\begin{pmatrix} 1&1&1&0&0 \\ 0&0&1&1&1\\ 1&1&0&1&1 \\ 1&1&1&0&0 \\ 0&0&1&1&1\\ \end{pmatrix}.
Associate to each row j an X-type stbilizer
M_j=\PROD{l=1}{5}X_l^{\delta_{jl}},
and to each column a Z-stabilizer
N_j=\PROD{l=1}{5}Z_l^{\delta_{lj}}.
The product of the matrix \delta with itself (modulo 2) effectively computes products of all the M_j operators with all the N_j operators. The i,jth coefficient in the matrix of \delta^2, has a value of 0 if M_iN_j commute and has a value of 1 if M_iN_j anticommute. In fact, since \delta^2 gives the matrix with all coefficients 0, each M_i commutes with each N_j. Therefore, the set Q generated by all such products of M_j and N_i forms an abelian subgroup of the Pauli group \hat{P}_5. Moreover, since each M_j and N_j square to +I, it is necessarily the case that -I\notin Q. Hence, Q actually defines a stabilizer group. By choosing linearly independent operators M_j and N_i, it is seen that the stabilizer Q can be generated by \{M_1,M_2,N_1, N_4\}.
Let C_1 and C_2 be a classical linear codes with parity check matrices H_1 and H_2 given by
H_1=\begin{pmatrix} 1&0&1&1&0 \\ 0&1&1&0&1 \end{pmatrix} \ \ \text{and} \ \ H_2=\begin{pmatrix} 1&1&1&0&0 \\ 0&0&1&1&1 \end{pmatrix}.
Notice that H_1 consists of the two Z-type stabilizer generators N_1 and N_4, and H_2 consists of the two X-type stabilizer generators M_1 and M_2 defined in (2) that together generate the stabilizer group Q. In this way, Q is the CSS code CSS(H_1,H_2). Here, Q=<S_1\cup S_2>, where S_1 and S_2 are the stabilizer groups generated by the Z-type and X-type operators, respectively. Namely,
S_1=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&1&1&0 \\ 0&1&1&0&1 \\ 1&1&0&1&1 \end{pmatrix} \ \ \text{and} \ \ S_2=\begin{pmatrix} 1&0&1&1&0 \\ 1&1&1&0&0 \\ 0&0&1&1&1\\ 1&1&0&1&1 \\ \end{pmatrix}.
Let G_1 and G_2 be corresponding generator matrices of the codes C_1 and C_2, respectively. For each code, since there are 5 physical bits and 3 encoded bits (H_1 and H_2 are 2 \times 5 matrices), both generator matrices have dimensions 3\times 5. These generators must satisfy the constraints
G_iH_i^T=0 \ \ \text{and} \ \ H_iG_i^T=0.
for i=1,2. The constraints form a set of k non-singular equations on n bits. It can be checked that the following two particular matrices satisfy these constraints:
G_1=\begin{pmatrix} 1&0&0&1&0 \\ 1&1&0&1&1 \\ 0&1&1&1&0 \end{pmatrix} \ \ \text{and} \ \ G_2=\begin{pmatrix} 1&0&1&0&1 \\ 1&1&0&0&0 \\ 0&1&1&1&0 \end{pmatrix}.
The rows of G_1 and G_2 form a basis of the code spaces C_1 and C_2, respectively. Hence, the span of each generates the entire code spaces. The elements of these code spaces are then
C_1=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&0&1&0 \\ 1&1&0&1&1 \\ 0&1&1&1&0 \\ 0&1&0&0&1 \\ 1&0&1&0&1 \\ 1&1&1&0&0 \\ 0&0&1&1&1 \end{pmatrix} \ \ \text{and} \ \ C_2=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&1&0&1 \\ 1&1&0&0&0 \\ 0&1&1&1&0 \\ 1&0&1&1&0 \\ 0&1&1&0&1 \\ 1&1&0&1&1 \\ 0&0&0&1&1 \\ \end{pmatrix}.
By associating a Z-type (or X-type) operator \overline{Z} (or \overline{X}) to each row of C_2 (or C_1), and demanding that \overline{Z}\notin S_1 (and \overline{X}\notin S_2) and also that \overline{Z} \ \overline{X}=-\overline{X} \ \overline{Z}, then the pair (\overline{X},\overline{Z}) can be made to correspond to a logical operation on a logical qubit. In this case, since there is only 1 logical qubit a single pair satisfying these properties is all that is needed. In this regard, choose
\overline{X}=X_1X_4 \ \ \text{and} \ \ \overline{Z}=Z_1Z_3Z_5
corresponding to the second rows of C_2 and C_1. Then indeed, \overline{X}\notin S_2 and \overline{Z}\notin S_1, and \overline{Z} \ \overline{X}=-\overline{X} \ \overline{Z}. Therefore, the pair (\overline{X},\overline{Z}) function as logical operators on the encoded qubit, and hence generate \mathcal{N}(S)/S\cong P_1.
In the classical linear code context, the distances of codes C_1 and C_2 are both given by d_1=d_2=2, which can be seen by examining the elements of C_1 and C_2 and finding the minimum weight of any non-identity codeword. For CSS(H_1,H_2), the distance of the code Q must satisfy d\geq min\{d_1,d_2\}=2. In this context, the distance of Q will be the minimum weight of an operator in \mathcal{N}(S)\backslash S, which by inspection is seen to be d=2.
In what follows, an algorithm will be described which begins with two parity check matrices H_1 and H_2 of a general CSS code, and computes a set of generators for \hat{\mathcal{N}}(S)/S grouped into pairs \{(\overline{X}_i,\overline{Z}_i)\}.
First, using H_1 and H_2 (matrices with dimensions (n-k)\times n construct generator matrices G_1 and G_2 (of dimensions k\times n) satisfying the constraints G_iH_i^T=0 and H_iG^T=0 for each i=1,2. Moreover, the rows of such G_i should be linearly independent. Such a procedure can be done in general using the Gram-Schmidt process.
Next, consider the codes paces C_i defined as the span of the rows of G_i, and also the stabilizer spaces S_i defined as the span of the rows of H_i. Then to find generators of \hat{\mathcal{N}}(S)/S, it suffices to choose pairs (\overline{X}_l,\overline{Z}_l) with \overline{Z}_l\in C_1\backslash S_1 and \overline{X}_l\in C_2\backslash S_2, such that \overline{X}_l and \overline{Z}_l anti commute, and all pairs (\overline{X}_l,\overline{Z}_l) and(\overline{X}_l',\overline{Z}_l') with l\neq l' commute. For k encoded qubits, there will be k many many pairs, corresponding to the logical operations applied to each of the k logical qubits.
\begin{align*} S_1=& Z_1Z_2 \\ S_2=&Z_2Z_3 \\ S_3=&Z_4Z_5 \\ S_4=&Z_5Z_6 \\ S_5=&Z_7Z_8 \\ S_6=&Z_8Z_9 \\ S_7=&X_1X_2X_3X_4X_5X_6 \\ S_8=&X_4X_5X_6X_7X_8X_9. \\ \end{align*}
Thus, the the dimension of the code space is 2^{9-8}=2, which implies that the code only encodes one logical qubit. In this case, \hat{N}(S)/S\cong \hat{P}_1, so \hat{N}/S will be generated by some elements \overline{X}, \overline{Z}\in\hat{N}(S)\backslash S, satisfying the usual Pauli commutation relations:
\overline{X}^2=\overline{Z}^2=\overline{I}, \ \text{and} \ \overline{X} \ \overline{Z}=-\overline{Z} \ \overline{X}
In this regard, let
\begin{align*} \overline{Z}=&X_1X_2X_3X_4X_5X_6X_7X_8X_9 \\ \overline{X}=& Z_1Z_2Z_3Z_4Z_5Z_6Z_7Z_8Z_9 \\ \end{align*}
which satisfy the commutation relations described above. Moreover, \overline{Z}\in\hat{N}(S)\backslash S. To see this, note that
\begin{align*} [\overline{Z},S_i]=0&, \ \text{for} \ i=7,8 \\ [\overline{X},S_i]=0&, \ \text{for} \ i=1,2,3,4,5,6 \\ \end{align*}
because each of these ease either a product of only X operators or only Z operators. The less trivial relations
\begin{align*} [\overline{Z},S_i]=0&, \ \text{for} \ i=1,2,3,4,5,6 \\ [\overline{X},S_i]=0&, \ \text{for} \ i=7,8 \\ \end{align*}
also hold, because the intersection of the supports of \overline{Z} and S_i ( for i=1,2,3,4,5,6 ) is always an even number of qubits. Likewise, the intersection of the supports of \overline{X} and S_i ( for i=7,8 ) is also always an even number of qubits. Thus, \overline{X},\overline{Z}\in \hat{N}(S).
Now, to see that \overline{X},\overline{Z}\notin S observe that the productS_7S_8=X_1X_2X_3X_7X_8X_9\neq\overline{Z}, which implies \overline{Z}\notin S. For \overline{X}, it is impossible to even generate an operator that contains all the factors Z_1Z_2Z_3 since the only stabilizers that even have nontrivial support on these first three qubits are S_1 and S_2, but yet S_1S_2=Z_1Z_3\neq Z_1Z_2Z_3. Therefore, \overline{X}\notin S.
Consider the binary matrix
\delta=\begin{pmatrix} 1&1&1&0&0 \\ 0&0&1&1&1\\ 1&1&0&1&1 \\ 1&1&1&0&0 \\ 0&0&1&1&1\\ \end{pmatrix}.
Associate to each row j an X-type stbilizer
M_j=\PROD{l=1}{5}X_l^{\delta_{jl}},
and to each column a Z-stabilizer
N_j=\PROD{l=1}{5}Z_l^{\delta_{lj}}.
The product of the matrix \delta with itself (modulo 2) effectively computes products of all the M_j operators with all the N_j operators. The i,jth coefficient in the matrix of \delta^2, has a value of 0 if M_iN_j commute and has a value of 1 if M_iN_j anticommute. In fact, since \delta^2 gives the matrix with all coefficients 0, each M_i commutes with each N_j. Therefore, the set Q generated by all such products of M_j and N_i forms an abelian subgroup of the Pauli group \hat{P}_5. Moreover, since each M_j and N_j square to +I, it is necessarily the case that -I\notin Q. Hence, Q actually defines a stabilizer group. By choosing linearly independent operators M_j and N_i, it is seen that the stabilizer Q can be generated by \{M_1,M_2,N_1, N_4\}.
Let C_1 and C_2 be a classical linear codes with parity check matrices H_1 and H_2 given by
H_1=\begin{pmatrix} 1&0&1&1&0 \\ 0&1&1&0&1 \end{pmatrix} \ \ \text{and} \ \ H_2=\begin{pmatrix} 1&1&1&0&0 \\ 0&0&1&1&1 \end{pmatrix}.
Notice that H_1 consists of the two Z-type stabilizer generators N_1 and N_4, and H_2 consists of the two X-type stabilizer generators M_1 and M_2 defined in (2) that together generate the stabilizer group Q. In this way, Q is the CSS code CSS(H_1,H_2). Here, Q=<S_1\cup S_2>, where S_1 and S_2 are the stabilizer groups generated by the Z-type and X-type operators, respectively. Namely,
S_1=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&1&1&0 \\ 0&1&1&0&1 \\ 1&1&0&1&1 \end{pmatrix} \ \ \text{and} \ \ S_2=\begin{pmatrix} 1&0&1&1&0 \\ 1&1&1&0&0 \\ 0&0&1&1&1\\ 1&1&0&1&1 \\ \end{pmatrix}.
Let G_1 and G_2 be corresponding generator matrices of the codes C_1 and C_2, respectively. For each code, since there are 5 physical bits and 3 encoded bits (H_1 and H_2 are 2 \times 5 matrices), both generator matrices have dimensions 3\times 5. These generators must satisfy the constraints
G_iH_i^T=0 \ \ \text{and} \ \ H_iG_i^T=0.
for i=1,2. The constraints form a set of k non-singular equations on n bits. It can be checked that the following two particular matrices satisfy these constraints:
G_1=\begin{pmatrix} 1&0&0&1&0 \\ 1&1&0&1&1 \\ 0&1&1&1&0 \end{pmatrix} \ \ \text{and} \ \ G_2=\begin{pmatrix} 1&0&1&0&1 \\ 1&1&0&0&0 \\ 0&1&1&1&0 \end{pmatrix}.
The rows of G_1 and G_2 form a basis of the code spaces C_1 and C_2, respectively. Hence, the span of each generates the entire code spaces. The elements of these code spaces are then
C_1=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&0&1&0 \\ 1&1&0&1&1 \\ 0&1&1&1&0 \\ 0&1&0&0&1 \\ 1&0&1&0&1 \\ 1&1&1&0&0 \\ 0&0&1&1&1 \end{pmatrix} \ \ \text{and} \ \ C_2=\begin{pmatrix} 0&0&0&0&0 \\ 1&0&1&0&1 \\ 1&1&0&0&0 \\ 0&1&1&1&0 \\ 1&0&1&1&0 \\ 0&1&1&0&1 \\ 1&1&0&1&1 \\ 0&0&0&1&1 \\ \end{pmatrix}.
By associating a Z-type (or X-type) operator \overline{Z} (or \overline{X}) to each row of C_2 (or C_1), and demanding that \overline{Z}\notin S_1 (and \overline{X}\notin S_2) and also that \overline{Z} \ \overline{X}=-\overline{X} \ \overline{Z}, then the pair (\overline{X},\overline{Z}) can be made to correspond to a logical operation on a logical qubit. In this case, since there is only 1 logical qubit a single pair satisfying these properties is all that is needed. In this regard, choose
\overline{X}=X_1X_4 \ \ \text{and} \ \ \overline{Z}=Z_1Z_3Z_5
corresponding to the second rows of C_2 and C_1. Then indeed, \overline{X}\notin S_2 and \overline{Z}\notin S_1, and \overline{Z} \ \overline{X}=-\overline{X} \ \overline{Z}. Therefore, the pair (\overline{X},\overline{Z}) function as logical operators on the encoded qubit, and hence generate \mathcal{N}(S)/S\cong P_1.
In the classical linear code context, the distances of codes C_1 and C_2 are both given by d_1=d_2=2, which can be seen by examining the elements of C_1 and C_2 and finding the minimum weight of any non-identity codeword. For CSS(H_1,H_2), the distance of the code Q must satisfy d\geq min\{d_1,d_2\}=2. In this context, the distance of Q will be the minimum weight of an operator in \mathcal{N}(S)\backslash S, which by inspection is seen to be d=2.
In what follows, an algorithm will be described which begins with two parity check matrices H_1 and H_2 of a general CSS code, and computes a set of generators for \hat{\mathcal{N}}(S)/S grouped into pairs \{(\overline{X}_i,\overline{Z}_i)\}.
First, using H_1 and H_2 (matrices with dimensions (n-k)\times n construct generator matrices G_1 and G_2 (of dimensions k\times n) satisfying the constraints G_iH_i^T=0 and H_iG^T=0 for each i=1,2. Moreover, the rows of such G_i should be linearly independent. Such a procedure can be done in general using the Gram-Schmidt process.
Next, consider the codes paces C_i defined as the span of the rows of G_i, and also the stabilizer spaces S_i defined as the span of the rows of H_i. Then to find generators of \hat{\mathcal{N}}(S)/S, it suffices to choose pairs (\overline{X}_l,\overline{Z}_l) with \overline{Z}_l\in C_1\backslash S_1 and \overline{X}_l\in C_2\backslash S_2, such that \overline{X}_l and \overline{Z}_l anti commute, and all pairs (\overline{X}_l,\overline{Z}_l) and(\overline{X}_l',\overline{Z}_l') with l\neq l' commute. For k encoded qubits, there will be k many many pairs, corresponding to the logical operations applied to each of the k logical qubits.