The higher temp thermal switches will help your problem, but, does not fix the main problem.
The stock regulator/rectifier only puts about 25 Watts of DC voltage towards the battery, or 1.85 amps @ 13.5 VDC, and the other 95 is AC voltage for the lighting system. Your fan is drawing roughly 2 amps.
I corrected this issue on my bike by shipping my stator off to UHE member sparks, and he rewound the stator for all DC use. Installed a TT universal 150 Watt regulator/rectifier, and ran the whole output to the battery, and then ran all the lighting off of the battery as well.
I have run all day in tight twisty conditions with the stock 85C thermo switch, stopped and started all day long with out an issue. Even with all the lights on there is more than enough left over wattage to run the fan and charge the battery at a very quick rate.
So, to begin with, you are at a bit of a losing battle with only 25 Watts going to charge the battery after using the electric start.
The main difference with the way Sparks does his re wind as opposed to just floating the neutral as a lot of companies do, is that by just floating the neutral on the original stator, you run the windings in series, which gives you about 120 VAC for the regulator to shunt down to 13.5 VAC before handing it over to the rectifier. With Sparks rewind, you end up with around 60VAC for regulator to hand off to the rectifier.
See my post here:
viewtopic.php?f=6&t=8852
Its a bit of overkill for most people but I put in a new loom as I was going to be running helmet lights etc.... The average person need not go to such extremes................sorry that I did not include a single line as promised.