If I may add this Dave, checking clearances is always the right thing to do, especially when using different pistons and cam plus when any decking has been done. Honestly this is part of engine building I find most interesting and rewarding and will leave no unanswered questions.
If you do measure, the piston to head clearance doesn't need a cam installed plus just the top piston ring is enough for this test. If you find from this that the MLS is too thick you can (either replace it) or use a different thickness viton/steel base gasket thickness (0.010 or 0.014" for instance) to allow a little extra piston crown proud of the deck. For a street engine don't run under 0.040" just because of stock rods & bolts. The pistons in my first race job just kissed the head (no damage) with stock rods and new 750F2 upgraded bolts/nuts. This with 0.036" clearance.
To be honest, until I witnessed this personally, I was never certain if OEM rods actually stretch, or if the bolts do, or if perhaps the piston crown "grows" upward. Now with Carrillo rods I run as tight as 0.027" without issue so it's evident rods and/or bolts can stretch a great deal. A missed shift allowing it to rev to the moon is enough. Short story... build ample clearance (1mm minimum) and the effect will be noticable.
Valve/piston clearance checking is most accurate if you use a degree wheel on the crank end and a dial indicator on a valve spring retainer. Setting the crank at different positions (8-10-12 degrees) before or after TDC depending of which valve, gingerly prying the valve open until it touches the piston gives you the exact clearance, far better than fooling with clay.
I didn't want to spew a bunch of crap & pile pressure on, but it sounds like you are leaning this way anyway. Good work, this will be a good engine.
