We can write the Fourier transform of $\langle 0|\mathcal{T}A_{\nu}(x)\psi(x_1)\bar\psi(x_2)|0\rangle$ as $$S(p) D_{\nu\alpha}(q) \ e\,\Gamma^{\alpha}(p,q,p+q)S(p+q)$$ where $S(p)$ is the full fermion propagator, $D_{\nu\alpha}(q)$ is the full photon propagator, $\Gamma^{\alpha}(p,q,p+q)$ is the proper vertex function, and an overall momentum conservation delta function has been dropped. Similarly, we can write the Fourier transform of $\langle 0|\mathcal{T}j^{\mu}(x)\psi(x_1)\bar\psi(x_2)|0\rangle $ as $$S(p)V^{\mu}(p,q,p+q)S(p+q)$$ where $V^{\mu}(p,q,p+q)$ is a vertex function that we want to relate to $\Gamma^{\mu}(p,q,p+q).$ The vertex function $V^{\mu}(p,q,p+q)$ enters into the derivation of the Ward-Takahashi identity in <PERSON> and <PERSON> on page 311, but the Ward-Takahashi identity is normally stated in terms of $\Gamma^{\mu}(p,q,p+q)$. Your conundrum (as I understand it) is that according to your analysis of the Schwinger-Dyson equation, $V^{\mu}(p,q,p+q)$ and $\Gamma^{\mu}(p,q,p+q)$ ought to differ by a factor of $Z_3$, but this contradicts the usual statement of the Ward-Takahashi identity where no such factor of $Z_3$ appears. I will argue from the Schwinger-Dyson equation that the longitudinal parts (in $q^{\mu}$) of $V^{\mu}(p,q,p+q)$ and $\Gamma^{\mu}(p,q,p+q)$ are equal, but that the transverse parts differ by the factor of $Z_3$ that you have found. 818
Since only the longitudinal part enters into the Ward-Takahashi identity, the factor of $Z_3$ does not inter into that identity. You may want to review page 246 of <PERSON> and <PERSON>. There they show that only the transverse part of the photon propagator is modified by the self-energy, but that in calculating <PERSON> diagrams we can simplify the analysis by including the self-energy in the longitudinal part as well because the longitudinal part does not contribute to the <PERSON> diagrams due to the <PERSON> identity. However, the <PERSON>-Dyson equation involves an inverse propagator which does not arise in <PERSON> diagrams and we need to reevaluate where the self-energy does and does not enter.
Specializing the Schwinger-Dyson equation to the case of $\langle 0|\mathcal{T}A_{\nu}(x)\psi(x_1)\bar\psi(x_2)|0\rangle$ and Fourier transforming, we have $$\tag{1} (D^{(0)\mu\nu}(q))^{-1} D_{\nu\alpha}(q) S(p) \ e\,\Gamma^{\alpha}(p,q,p+q)S(p+q) = \ e\, S(p)V^{\mu}(p,q,p+q)S(p+q)$$ where $(D^{(0)\mu\nu}(q))^{-1}$ is the inverse of the non-interacting photon propagator. 469