FWIW,
Send the stator to UHE member Sparks for a rewind of the ignition part of the stator, that is the part that goes bad.
The power supply or alternator aspect of the stator seems to be pretty good.
Since your bike is an 01, it uses just a small portion of the stator/alternator output in rectified to DC for battery charging, the rest is for running the lights.
The advice I got from Sparks was to tie the two outputs of the alternator together (check with him to make sure of wiring ) and use a Trail Tech universal regulator/rectifier to feed not only the battery, but to run all the electrics off of DC rather than AC.
The big difference here is that if you are running your lights with the AC side, and its night time, and you kill the motor the lights go out!
I converted my 04 550 to all DC. The big problem people were having in........I believe 06, is that with the redesigned tank, one could now install a radiator fan, and the same AC/DC split was true on these bikes with the new Kokusan ignition. So if you were riding slow technical stuff and the fan was on all the time, when you hit the electric start the battery was dead b/c the fan drew more power than the rectified AC to DC conversion.
I had Sparks rewind the Kokusan ignition completely for more power output at a lower voltage for the regulator to handle. A lot of guys were just floating the neutral, as that was the easy way, but, you ended up with roughly 120 VAC that had to be regulated down to 14.5 volts before it hit the rectifier.
With Sparks winding set up it put out 60 VAC that was then regulated down to 14.5 VAC and then, in my case, it hit my TT universal rectifier to deliver 120 watts of power to the battery.
So in the end, I could have all the lights on, fan running all day, and it was not even stressing the alternator.
Besides that, it seems like you upgraded to the 2003 rocker arms which was essential, as well as the swivel foot valve adjuster stem. Since you have gone to the newer head as well, if you just put some sort of filter on the breather tubes of the carb, your valve clearance check/adjust intervals should be greatly extended. The super fine grit that gets pulled into the carb through the vent tubes acts like lapping compound to the valves and the valve seats.
There was also an upgrade on the cam chain tensioner as well. It has the "elephant" foot on the end, and I believe that one could put a later model cam chain slider in as well.
If you ever hear a knocking noise check the primary nut on the crank. Never had the problem myself, but, some reported to have it come loose.
Your bike has the single counter balancer bearing that was changed to a double bearing in 02. However, if you keep the oil changed this will greatly increase the life of the whole bike as well as the CB bearing. Use good oil too.
I put a lot of racing miles on my 01 501 in the desert. Had one stator go bad that I sent to Sparks and no more issues after that. Never had a problem with the CB bearing though.
If you have any questions feel free to ask........I still have my 01 501.