I've been a Certified Master Engine Machinist for more years than I can count - The "rule of thumb" is .0015" per bore inch if you have no specs at all. The material that the piston is made from is a BIG determining factor in piston clearance. Old-style aluminum pistons with no silicone in the allow expand a LOT! Heating a 3" piston on the bench with a heat gun has shown me up to .006" EXPANSION - this would NOT be a good deal in a bore where you have .002" clearance! The theory is that you let it warm up SLOWLY and the piston won't seize, hopefully. High silicone alloy pistons (Keith Black Hypereutectic for instance) expand very little - and the expansion is quite carefully controlled with the casting of the piston. It is not uncommon to clearance these types of pistons at .002" in a four-inch bore. Forged pistons require a bit more claerance as well as they expand a bit - in a three-inch bore, I'd not be afraid of up to .006" depending on the piston type.
All-in-all, the thing to keep in mind is that the bore is STRAIGHT and ROUND. These two factors allow the bore to be "loose enough to run" without risking piston slap or a tendency to smoke like a Southern Barbecue grill on start up. If you are a civilsed rider - go tight - if you plan to run the eyes out of it - loosen it up just a little and enjoy! I hope this helps a little!