Heuristic solution

$J = \mathbf{C}^g / \Lambda_J$, the period lattice $\Lambda_J$ computed numerically, to high precision, from a basis of $H^0(C, \Omega_C)$.

By picking a $k$-basis for $H^0(C, \Omega_C)$, we have

$$\operatorname{End}(J) = \left\{ T \in M_g(k) \mid T \Lambda_J \subset \Lambda_J \right\}$$

Hence, if $\Pi$ is a period matrix for $C$, i.e., $\Lambda_J = \Pi \mathbf{Z}^{2g}$, then we are reduced to finding a $\mathbf{Z}$-basis of the solutions $(T, R)$ to

$$T \Pi = \Pi R, \qquad T \in M_g(\overline{k}), \quad R \in M_{2g}(\mathbf{Z}).$$

The Galois module structure of $\operatorname{End}(\overline{J})$ is given via its action on $T \in M_g(\overline{k})$.

Heuristically, via lattice reduction algorithms, we can find such a $\mathbf{Z}$-basis.

There is no obvious way to prove that our guesses are actually correct.