Not uncommon to have to grind a rod bolt or two. Generally #2 and #7. I suggest you let a knowledgeable engine shop assemble it if it seems too much.

It's not very hard to do. I use a paint marker to mark where it needs clearanced, pull the rod/piston assembly out and grind just enough to get .050" clearance. I use plastic tie straps as a measuring device since it's hard to get a feeler gauge in that area. You don't normally remove enough metal to throw the balance out of whack.