Yup everything was torn down and thoroughly cleaned (pressure tanked and brushed). Rods unfortunatly I think were the problem.
Machine shop checked them for straight and round but I can't help but feel that they were slightly oversize and not caught before the last assembly. Really looks like there was too much clarance right from the start. My bad too as I didn't plastigage them after I got them back from the shop, I just trusted that everything was to spec. Like I said, I have never had reason to not trust the machinist I have used for years in the past so I just didn't think it was necessary. I will in the future though just to know for sure.