The needle didn't move at all on all mains so I know the crank is good. Talking with Mad, I think we got it down to cap distortion when tightened.
Not necessarily true.
The needle likely isn't moving because the journal is being backed by the bearing, it's only indicating the OD of the journal.
To check if the crank is bent requires supporting the crank as if in v blocks, by removing the shells in the center, but pay attention closely
I have found not only 1, but all of them on the shelf likely to have this gem of a problem at a crank supplier, and it's possible you have it also. Could be same place in MN.
Engine in question had a tight spot, also binding near the center.
Supported by the end bearings the error was worst from 4th to 1st journal but still with very slight edge contact on the rear shell. Hmmm.
Supported by 4th and first journal showed all DEAD ON...except the rear journal was eccentric by more than the bearing clearance. Bingo.
The crankshaft was not properly set up on the grinder, and it's own counterweights were wobbling the crank eccentric while grinding.
The next 2 cranks had the same problem...
To be clear, it doesn't easily show up in that case because the rear bearing locates the journal and forces the rest of the crank to run around it.
Not saying you have the exact same problem for sure, but it's easy to check.
One major difference I'll point out is that I used a test indicator with a much wider sweep across the gauge.
Your 1" drop indicator is probably not sensitive enough to pick up this problem, as it only takes 1/2 of the clearance (plus the interference amount) to run an eccentric journal into the bearing.
You are looking for deviations from .0012-.0015" or so.
I also believe your crank clearance is too tight.
There are a few ways to correct this depending on what you find.
If you try to run it like this, the crank will self clearance itself
I will say that your pics suggest a distortion/out of round condition with the main caps.
You could have a bit of both, with the problems "finding each other"