You know, that is exactly what I was considering writing here. Proper polishing should work, so long as the outer rounded bearing journal is not cut, whatsoever.
When contacting the expert in Helena, MT who specializes in Crankshaft work, he explained the process of the Big Hammer to straighten anything out. Sounds crude, however if you know what you doing from years of re-working journals and ploshing everything, he explained it's really simple, if you have the touch.
If you detect a bent rod, have no idea if the crank needs to be hit in a few spots or might have been accidentally dropped during rebuild, you just don't know what you have anymore.
My advice is either bite the bullet when you buy new stronger rods and forged pistons, moly rings, wrist lock pins, (squirters if you can afford them), is either:
A) buy a good remanufactured Crank,
B) have your's reworked and properly polished by somebody who does nothing else,
C) find one on sale from a major online store.
You don't need triple layer bearings unless you race it. If it is a slightly looser fit in the bearings, vs what GM originally had it set up with, say .005-.015", or even .025"more slop, you might be OK.
The book says .004" is NO-GO everywhere.
My guy insists you end up with more than that everywhere the first five minutes of break-in.
Only years of rebuilding and actually knowing what you can get away with, and where, works here.
My expert builder (30 years Diesel engines and HD Truck tranmsissions repair) explained how many years of rebuilding everything, including high HP diesel engines and performance race engines, he ALWAYS considered GM's effort to restrict the rotating assembly with extremely tight bearing tollerances, as un-nessesary and prone to substantial break-in wear.
We went through the GM Service manuals verifying every tollerance in the rotating assembly four times.
He promised me, he rebuilt a lot of older engines, with a HQ Hone, and reloaded stock bearings with a slight amount of wear spacing, polished what a lot of critics said was a bad crankshaft and the engines would run very well. Thousands of them.
It's got to be straight. Pulled from the exact engine with spin wear and protected 100% of the time, it's out of the engine.
My crankshafts, uncertain which I would be using, I made a dash to a very remote part of the shop, hid and protected them under cover.
Not left standing on end, where the forklift can hit and knock it over.
If you polish it and have it straightened, you could save a lot of money.
If it needs to be cut, your crankshaft specialist will have a nice remanufactured unit already for you, most likely.
If there was zero chance it was dropped, or bent, you could easily use some 0000, clean it up for street use and run it.
The mis-matched caps is an issue.
GM is known for alignment problems if you swapped the caps. If they walk, all your measuring is for nothing.
There's a lot to be said for careful polishing, repalcing the bearings, verify everything with plasti-gauge and verify rotation with new rods.
You already took it to a new machinist, is your new situation.
His protocall is now your best solution.
Especially if he hears you got a refund from somewhere else.
He's going to cover his liability and it's going to cost a bit more to do it "his" way.
This is why I refrained from commenting, so you don't get your new machinist upset with you suggesting short cuts to save money.
Whatever you do, don't argue or suggest anything to do with proedure with this one.
It seems the more they charge, less likely they are to even listen to suggestions from the customer.