I've mentioned it'll run like a bandit without "tightening" anything. Consider what Honda built, 0.016" (often) down the hole, a 1mm head gasket and way adequate valve piston clearance, similar to what you just saw. These kind of ultra safe clearances ran reliably well. However there was virtually no effect of squish at over 0.050".
You're building a signature engine and have the opportunity to tweak some of those clearances to develop a little extra. Since you asked.... I would use the thinner base gasket (0.010") to bring the piston compression height close to deck, then use a 0.040" MLS head gasket. That way the head gasket thickness equals your squish clearance. Safe but should help.
I have seen piston/head kissing in my race engine when I increased the rev limit instead of changing sprockets the last race of 2011, this with 0.036" clearance and stock rods, & new F3 bolts. I cannot say if the rods stretch, or bolts, or both, or if the piston crown grows exponentially with more heat and 12K rpm, but it was obvious to me that there is a definite need for clearance. (now with Carrillo's I run much tighter so I expect the stretch is rod related)
One other thought is with the 650 head. Unless your bore is larger than the combustion chamber there is difficulty gaining squish advantage with that hemi style chamber. The 550's use that cast in squish shelf and in my opinion, with the right piston crown, there is hidden power available. The beauty of the 650 is increased valve size/improved ports. I have my own ideas how to improve this chamber but money always gets in the way!
All the more reason to check with solder or clay after you choose which gaskets to use. Be thorough Dave and it will be great.
Finishing this job will be carb selection, what do you have planned?
