Originally Posted by 350TSS

Welcome, I think your analysis is correct - poor running only when hot is probably electronic related, coils, exciter boxes (next to the coils) or ignition pick ups (located in the alternator case).
The only other possible cause I can think may affect running when hot would be too tight valve clearances. Checking this should not cost anything (unless you find them out of tolerance and need to buy replacement shims) but is a bit fiddly and time consuming. There a plenty of videos on youtube on how to do it. If the clearances are in tolerance then that can be eliminated as a possible cause.
If you have other Monsters then it would be worth swapping compatible components on the 900 with known working ones on one of the other ones that will narrow down which bits really do have to be bought as replacements.
If you do need new coils Exactfit UK do higher output ones (same as California cycleworks) for a reasonable price compared to Ducati originals