Just read your post again. The machine shop turned one rod 180 degrees? If so was the chamfer facing the wrong way before or is it the wrong way now. I don't pretend to be and expert on anything and don't make it a habit of telling people what to do, but if that was my engine I'd pull the rods off and make sure the chamfer is facing the correct way and the pistons are hung on the rods correctly.
FGF member Medhat68 has a piece on his website "Alberta Firebird Homepage" about the correct alignment. I'd advise you to read that, it's good info. And he's got a lot of great pics of his build.