This doesn't sound too good to me. As was said before the engine shouldn't make any noise except out of the tail pipes! If it were upper end noise I would ask if the lifters were primed before installation. If it truely is a bottom end noise then I'd suspect loose clearances. If the rods were over torqued then possibly there was some damage done to the rods or the rod bearings to cause this. Over torquing, then loosing them, then retorquing to the correct specs may be causing the clearance issues due to rod bolt stretch or bearing distortion. It all depends on how tight they were made in the first place. I'd check the obvious first like loose bolts on the converter, flywheel or maybe the accessories on the front of the engine (you never know). Then check that crankscraper for clearance and/or interference. If these things don't fix the problem you'll have to pull it down and check clearances internally. Good luck and I hope its an easy fix.