Rotating assy balance

For starters you should not be switching rod caps around. A connecting rod and rod cap is machined and align bored as an assembly. Switching caps around would require the rod to at the very least be checked with a T gage and a micrometer to be sure its in spec. At the worst, align bored and honed to get it in spec. Otherwise the clearances can be too tight or too loose on the rod. Both lead to disaster.

This all being said, the machined pad on the rod cap is where the excess material is removed to balance a connecting rod. If your machinest wanted all that moved around, he should have done it, resized the rods with the issues, and re marked the rod/cap assemblies.

I have taken at least a dozen engines apart in my lifetime and i never have seen rod caps with varying heights all in one engine like that, but that's not to say this didnt ever happen.

How far off was the crankshaft? Was there a lot drilled out of the counter weights? A lot added in the form of mallory slugs welded in?

You probably payed good money to have this done with your rods. The whole magnaflux, check for straightness, shot peen, etc route. Honestly you would have been miles ahead with a new set of Eagle forged I beam rods with bushed small end and ARP bolts.

Maybe somebody else can chime in with more information on this than what I got. Heck, I'm an amateur though, I dont assemble em weekly like some of the racers around this site do, what the hell do I know.

Hope this helps
Matt