I'm not sure whats causing your difficulty, but I always assemble everything loosely until everything is attached...then you can tighten everything up. Try hard not to strip out the stud holes on your engine...that would be considered a bad day.
Well, fire the engines! Spur this iron space-pony on!
The stud from the picture. I'm pretty sure I broke it because that threaded part never went through the head of the stud...
Negative! You just backed out the stud. Both ends are threaded so... yeah. Grab you a pair of nuts, run one on to the stud most of the way, then follow it up with another. Drive the nut furthest from the head against the next nut, and the stud will start turning in. The nuts might lock together giving you a fit taking it apart, but if you can get a wrench on both you can break the lock and back them out without disturbing the stud.
if you love your motorcycle, set it free.. if it comes back and hits you.. you highsided
Can't I just leave it for now like that? I think I will... It only happened for two of the bolts... The rest are fine...
Well, it depends. i wouldn't.
The right way to install headers is to back out 7mm flange nuts from studs, clean studs with wire brush (if came out) and put them back into the head, install new header gaskets ($3/ea) and new flange nuts (not mandatory but I would for $3/ea). I would also replace studs... why not for $3/ea? $60 in parts total and done once
It's impossible to torque flange nuts to the correct value with them being fused/rusted to studs, therefore one would never know if gaskets are compressed enough to seal the header.
In case you reused old header gaskets (which is doable), old flange locations (nuts fused to studs) are definitely not sealing properly at this point.