Are you using the 12" long feeler gauge stock like we did back in the dark ages? The last time I tried to buy some of those feelers, nobody was stocking them anymore, and most of the younger counter guys at the parts stores didn't even know what I was talking about.
Most machine shops used to hone a piston fit of one thousandth per inch of bore size, so a 3 1/2" bore piston would have a .0035" skirt clearance. That's a litle loose, in my opinion, but I've built a lot of 4" bore 350's with .0025"-.003" skirt clearance and had no problems with piston slap or excessive oil consumption. Modern hypereutectic cast pistons can be fitted much tighter that those specifications, but a couple of thousandths or slightly more skirt clearance doesn't spell disaster.
Jerry