Can you explain this a bit more...Id like to learn more and im sure others would as well.

"Think we figured it out with more investigating...the bearing caps weren't sitting correctly. High spots in the bearing saddles."

Was this a junkyard block? How did you set the clearances?

Upon assembly with the caps set on the register other then maybe a tap with a very small screwdriver sized rubber mallet they either fit correctly or they dont.

Id think you should of been able to pick up on something upon assembly.