I know you are not the OP but, I wanted to add my thoughts
to your observations.

He should also use one of those special low tension valve
checking springs when checking valve-to-piston clearance.
That way, the lifter won't be compressed by the valve spring
as it opens.  Also, cutting a head that much can really
screw up valve train geometry for a leaned on engine.  This
has to be corrected somehow during the build.  This engine
probably should have been built with only one cylinder to
start  to find the worst possible case of piston contact.
If that clears, bring 'er up to TDC and manually open the
valve until it either bottoms the spring or hits the piston
while watching a dial indicator to see if that distance is
greater than the effective lift at the valve.  If that
doesn't pass, the piston valve releifs will need to be
machined for clearance assuming there is enough meat in the
piston crown to allow this.  If not, either the pistons or
the cam must be replaced with something compatible.  Cutting
the pistons may also affect engine balance which means they
should be checked for equal mass after machining is
completed.

All that said, it never ceases to amaze me how many folks
decide they like some combination and proceed to assemble it
without bothering the so much as find out whether the parts
are reasonably compatible.  I find it is fairly easy to
gather information to educate myself from other peoples
mistakes.  Most rodders are glad to share their experience
with various combinations.  The tech support guys at most
cam and psiton suppliers have a pretty good idea which parts
will or will not work w/o mods and whether the mods will be
extensive or minor.

Lugnut