I have a Haynes and Chiltons manual, and they both say that the piston-to-cylinder clearance should be .0006" to .0014" (I might have the 6 and the 4 backwards). Is this right? The old rule of thumb is .001" per inch of bore. That would mean about .0035" of clearance would be right. Their numbers just sound awfully tight to me. Thanks for your help.

If you know which piston came out of which bore just return them to their originals to be safe. Make sure there isnt significant skirt scrape on the pistons and you should be fine.