Hi Austin – first, thanks for the positive feedback about the course! That’s very rewarding to read 🙂
Your eye issue should be relatively easy to fix. You definitely want to fix it before sculpting detail because adjusting the mesh (especially adding new mesh parts/verts) can ruin multires information.
Have you tried re-doing the part where I sewed a sphere to the interior eyelid? It’s a pretty straight-forward operation where if something went wrong, like duplicate verts, simply reperforming that procedure should resolve it.