I recently got my Form 1 recore back.
A flat bar was included to keep the baffle clips aligned when assembling.
I've found that I can't remove the bar as it binds up. It's probably not a big deal if the clips are a few degrees rotated, right?
Am I doing something wrong when spinning the end cap down?

If you clock the last baffle (or two) out of alignment counter clockwise (View from the front cap) and lube their mating surfaces, as you bring the front cap into tightness the last baffle or two should come into good enough alignment. Lube the alignment rod as well.  As long as you can withdraw the fixture rod a little clip misalignment is fine. In fact, if you can’t hear a difference the main benefit to clip alignment is POI shift repeatability. If you aren’t aligning to an index point on the tube on a precision host you probably wouldn’t notice. For example a subgun can popping water jugs at 15 yards with mag dumps it doesn’t matter. Sometimes field engineering can tolerate: measure with a caliper, mark with a crayon, cut with an ax assemblies.

ETA: after shooting a stack can compress a tiny bit, peening or forming spacers mating surfaces tighter. You may find the problem goes away.

This was my experience with my form 1 can (single radiused clips). only thing is that sometimes pre-staging isnt an absolute science, so you might be playing with alignment a for a few minutes while attempting to get it "perfect". my last and second to last cones are about 10 and 5 degrees off alignment respectively. I might try to get them properly lined later, but I think its good enough.

There is no need to spend any time getting bore asymmetries perfectly aligned.  Close enough is good enough.  Prob 20-30 degrees isn't going to make any observable difference.