So, I was very wrong to be worried...and I am very impressed.
I went back over the crankshaft and re-measured everything. Made very sure I was getting the measurements using the same amount of drag across the journals with the mic...

Main Journal Measurements:

#1 - 2.7493
#2 - 2.7494
#3 - 2.7492
#4 - 2.7493
#5 - 2.7493

only .0002" variance between all journals

I set up my dial bore gauge off of each main journal measurement and came up with the following bearing clearances:

#1 - .0024
#2 - .0024
#3 - .0020
#4 - .0028
#5 - .0028

I'm going to swap the lower bearing halves for 1 and 2 with 4 and 5 and see what happens. Ran out of time tonight.

The issue is me being rusty, not the machine work.