To resolve the deck height problem, you can also offset turn the con rod crank journals. If the journal needs a .010 cleanup, offset it .030 to pull the piston down .020. The journal gets turned .010 on one side and .030 on the other side.
For what it's worth, my 200ci pistons stick out of the bore .006". I wanted to experiment with options to take up some of the extra squench created by composite gaskets. It hasn't broken yet - about 4000 miles.
Off-set grinding the crank rod journals also works in reverse. You can either raise or lower the piston.
Ain't it fun???
Good Luck