Upgrades in my opinion based on what I have tried on my Mark II 850. Some produce "upgraded" performance by returning the bike to oem specs:
One of the various front Fork mods (I used the Fauth and it's great)
OEM wheels/tires (yep, changing back to them was a decided handling upgrade and also allowed removal of steering damper)
Trispark (but still in the test/monitoring mode) othewise upgrade by going back to oem points/AAU.

Remember that ONLY points allow you to actually time each cylinder individually (though you will have to use a degree wheel to determine the accuracy of the oem marks for that purpose). All Electronic units that I am aware of are wasted spark so that option does not exist.
For disc brake: SS line, sleeved mastercylinder at MINIMUM; Brembo MC for modern braking performance
All new internal rubber parts for ISOs.
Resleeved AMALS to return them to original clearances. Amals will idle smoothly at 600 RPM if set up and operating per specs. AFAIK, no one argues about their WOT performance.
That's pretty much it from my experience, anything else is just normal repair/parts replacement. Obviously some items are largely personal preferences for various items such as brake pad material, sealed bearings vs regular, Various ISO clearance (read everything from .001 to the oem .010) and other stuff like that.