Engine decking issue(help)

several issues here
first I usually did the trial assembly after line bore (and I do not trust line hone)
I'd have done the rods on the tobin-arp and they would all be the same (maybe bushed to the max for "stock")
.010 is a bunch do the trial assembly with the longest rod/piston combo and find out per YR
using a bridge you can check both sides of the piston to get a hint of square
Cometics require smooth- as YR says all can benefit
out of the hole is ok- you can change the gaskets I have a closed chamber 440 .015 out with .050 gaskets
My shop had the BHJ tooling- most good shops around LA have it but we did just fine before tooling was available- just takes more time
cam tunnels are not always straight with the mains- especially after a quickie line hone
calipers for a quick check but not for low corners