Good news on the bolt!
You can start the engine and assess the condition of the stator with a voltmeter on the battery, as chewy stated I had the rotor slide rearward when my 1100 did this, it damaged the stator, no charging and the engine had to come out. You may be lucky and the rotor didn't slide enough to damage the stator and the alternator is still good, if that's the case I'd try a jerry-rigged fix before having to pull the engine.
I'd try to clean up the threads with a sharp pick to get remnants of the cap out of the threads in the cover and see if you can get a new cap to fit. You could then try to fill in the broken out area with JB weld, or even try to glue in the broken piece. Might have to file the threads off the little piece if you can't get the threads to line up correctly.
There's no oil to speak of getting to the back side of that cap with engine running so leaking won't be a problem, the fix doesn't have to be perfect, it just needs to cover the hole enough to keep dirt out. This would save pulling the engine and trying to find another rear cover.
However, if no charging the engine will have to come out anyway.
Good luck!

A local inventor has figured a way to turn a sausage grinder backward to manufacture pigs.
♫ 99 Little Bugs in the Code, ♪
♪ 99 Bugs in the Code. ♫

♫ Take one down, Patch it around, ♪
♫ 127 Little Bugs in the Code. ♫ ♪

~Mark