2003 Ultra Classic engine backfire when upshifting

get a good tuner and that should fix the problem. Sounds like running to lean.

Thermal safety cutout is shutting down ignition, if you don't feel the engine is that hot replace thermal cutout and relay

Backfiring is usually the result of ignition timing that is advanced too much. Retard the timing a bit to see if it stops. A tune up should solve this if you can\'t.

As a Harley tech I have no idea. You would be better off posting this under a BMW category.

You can try lucas trasmssion fix.

A few questions first, Is it hard starting,lag on acceleration,engine hotter than normal?

Because the clutch is a wel clutch it needs some revs behind it. On the upshift try to preload the shifter, in other words pull slightly on the shift leaver before pulling the clutch in. This should stop the clunk on the upshift. On the down shift try to give it a rev just before pushing the lever down, the idea being that there are some extra revs to assist the gear change. I gather the bike is reasonably new, this is pretty normal and will loosen up as the bike runs in. If it is worrying you, mention it at your next service as the clutch plated could be dragging causing too much load to shift correctly.

excessive fuel in chamber can cause that

In reality, the gearbox was never designed for power shifting. Time is lost in trying to do a power shift with the tranny not willing to cooperate. Give yourself a break and use the clutch. It beats a missed shift every time.