The pistons will tell you which way faces front, and the rods will tell you what side of the journal pair they should be on....
I've been drinking for quite a few hours but I'm pretty sure that's not enough to be able to identify each piston with each hole.
Just to make sure we're all on the same page, you pulled the pistons/rods out of your engine without marking them and now you don't know which is what. Is that correct.
and to your original question, are the big ends resized and round now? If so, you need to spend a LOT of time making sure there's no honing stone grit in the wristpin area. If so, your engine will eat itself with a quickness after you put it together.