i'm running a .060 over stroker with no issues. i bought a balanced rotating assembly from eagle with all the bottom end stuff i needed. had the block prepped by the pros, and put it all together myself. when its days are numbered i'll order one of these,
http://www.summitracing.com/parts/SUM-150100/
and some .03 over pistons and call it a day.
the problem is if its already .06 over and needs a little freshening up on the cylinder walls, you could run into an issue there.