Don't know how far you're planning to have minicel under your braces, but it's pretty flexible. You shouldn't have any problem. Worst case, you can cut it at an appropriate spot and reglue it once in place.

Shouldn't be a problem with the bulkheads, either. I've put a foam one in a plastic boat, and a wood one in my Osprey. Both slipped past the footbrace rails without a problem. Just a matter of finding the right angle. Gets trickier the closer you want the bulkhead to the rails, but a couple of inches is plenty of room.