Need some advice with my piston swap.

Better off having the block checked by your machine shop for taper, etc. Bore gauge is going to be much more reliable in this case. Then choose your pistons. Do not buy until they check the block.

Most pistons now have the clearance built in. This means that if they're .040 pistons and they need .003 clearance, they're machined to .037 & with them being cnc now, they're all within 1/2 thou at most.