As a follow up, my original solution of twisting the longeron a little to make it line up wasn't the fix I needed. The twist cause the longerons not to be parallel with each other when a ruler was put between the two. i.e... they looked like they were pigeon-toed. I worried about this propagating to alignment issues with mounting the horizontal stabilizer later on.
To trim down the F-711A/B bulkheads without disassembling anything or marring up the F-711C bars, I used this trick:
I was able to slide a piece of thick plastic between the F-711A/B and the F-711C. This acted as a guard to keep me from scratching the F-711C bar as I filed. After a few minutes, everything fit nice and snug. I supported the aft fuse by resting it on the end of the F-711C bars so that the longerons could hang down. The only disassembly needed was a few clecos holding the side skins on the aft fuselage.