first keep in mind pistons are a bit barrel shaped vertically (or looking from the side) and oval ,looking down from the top, as the top expands more as it get hotter, and they don,t expand equally as they heat up, your more than likely well within the acceptable range,obviously you can call the manufacturer and get their feed back if your concerned and just as obviously you could hone the bore a bit larger for more clearance, but given what your saying IE your using a feeler gauge and getting about .003 side clearance, (which is more than likely a tiny bit larger because of the way your measuring and the tool used) I think your withing the acceptable range.
but I would call the manufacturer if your concerned, if it was my engine I would have already done that and asked a dozen questions., but after talking with dozens of tech guys Id bet money that you could ask 20 different tech desk guys and get similar but never the same answers talking any of them on any given day,even if you call back and talk to the same guys on different days and probably not the same answer from the same guy twice.
Piston-to-Wall Clearance
The right clearance between the piston skirts and the cylinder walls is absolutely essential. If the
piston-to-wall clearance is too large, the pistons rock back and forth in the bore. This prevents the
rings from sealing the cylinder properly, and can crack the skirts as the piston slaps from side to
side. If the clearance is too small, the piston will literally stick in the bore, scuffing the skirts and
destroying the wall finish. There’s a thin line between too much and not enough, but providing the
correct running clearance pays dividends in both durability and horsepower.
Piston skirts are slightly elliptical when
measured at room temperature. This oval
shape is the piston’s “cam grind.â€
A “barrel face†piston has a skirt that
bulges outward in the center. Because
of this complex shape, it is essential to
follow the piston manufacturer’s
instructions when setting the piston-to-
wall clearance.