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Oct 14, 2022 at 17:45 comment added Kapil The example for $g=1$ is also explained in an older MO answer in a different and perhaps easier way.
Oct 14, 2022 at 17:35 history edited Kapil CC BY-SA 4.0
Note that the answer is not complete for the original question.
Oct 14, 2022 at 17:31 comment added Kapil I missed the point about the need for the variety $Y$ to be affine!
Oct 14, 2022 at 17:28 comment added Sam Gunningham @aglearner I believe $Y$ is not affine (giving an example of a non-affine algebraic stein manifold). See e.g. Remark 7.6 in this paper of Neeman jstor.org/stable/2007052
Oct 14, 2022 at 14:43 comment added aglearner Dear Kapil, thank you for writing up details for this nice example! Note though that in my question both $X$ and $Y$ are affine surfaces. Certainly $\mathbb C^*\times \mathbb C^*$ is affine. But how do you prove that the algebraic moduli space of flat connections on a line bundle over $E$ is an affine surface? I.e why your $Y$ is affine?
Oct 14, 2022 at 14:12 history answered Kapil CC BY-SA 4.0