Went out there after work and nosed around. I examined the area where the manifold was and took a couple pictures - attached here - where the manifold was attached. Since that was the original problem, I assumed that's where my mechanic found the holes.
Granted, I don't really know a dang thing about Atomic 4s aside from the fact that mine hates me and has since I bought my boat last year, but everything looks normal to me.
Stopped by a local bar / restaurant. Asked the bartendar if any mechanics come in there. Left my number for one she said comes in every afternoon for a drink on his way home. Maybe he'll call tomorrow.