If the EGT is bad without NO2, then as you say probably the carb, which as temp increases as fuelling gets lean & I saw a max of approx 400F difference, then either one is really lean or one is really rich !
If it was mine, I'd add a O2 port to each header & then run the bike with the O2 senor on one pipe or the other on a repeatable run, NO nitrous, log 3 runs on each port then compare & adjust. Then repeat with NO2 at various levels, just to check BOTH cylinders are working at their maximum performance & at a similar level.
Main jet or needle position changes will be required to balance both intakes. I'm assuming you have the butterflies balanced already.
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