Yea never run a piston that's too tight it could seize up in the bore when it expands and ruin all your hard work. can you re arrange the pistons in the bores to make it in spec? is it just one big piston? buy another? if not it just needs a little platu hone to get it in spec. you can do it yourself, it is a learned skill and nice to practice on a junk block. id feel alot better about it if all the cyls were honed the same way, you don't want to hone any more on the ones that are ok. I would take it back.