Mike,
Sounds like maybe you're second guessing your machine shop? A little bit? Or, they don't have those types of answers for you?
Maybe you need to talk to someone like Tom Lucas at FE Specialties. I can tell you first hand, he is a very knowledgeable and meticulous engine builder. When it comes to engine building, I always recommend working with a professional rather than winging it on your own and piecemealing information.
Tom not only fixed a complex problem with my engine, he found an unrelated catastrophe waiting to happen that no one else realized.
Good luck, John