Your machinist works for you...make sure he understands that. Do your own research on the build, use the recommendations from the parts manufacturers as far as clearances, tolerances, etc. make him do it your way, not "the way he always does it"...and check his work.
I agree your machinist works for you, but having to tell him how to build an engine specific to your needs is like telling your lawyer how to defend you in court, your doctor how to do surgery, or your accountant how to prepare your taxes. You should give him your details on what you expect and what you want it to do in your application, and they tell you how to make that a reality, and
how much it's going to cost to get there.
I agree with Crewchief, if you have to tell him what the clearances should be or "boat build spec" v.s. a car motor, you're probably in the wrong shop.