How much piston material did you remove? Put the piston at TDC and look at the bottom edge of the sleeve for any air gap between the bottom of the piston skirt and lower edge of the sleeve.
You might just have SPI'd your engine (S.P.I.= Sub Piston Induction )
SPI is an old racers trick...it might not make any difference, or...??? There was a long thread a while back about improving mileage or something, that entailed cutting the bottom of the piston on the E. side...but how that might work with your engine and pipe is the question.

If you didn't need to remove much material, and didn't bend the rod then I'd say try running it and see if it still runs o.k....take it easy at first just in case.