Seeing as no one else answered....
You could try putting a fan on the controller and see if it stops or changes the frequency of the problem.
If so then I would think that would pin point a thermal shut down condition.
Did you ever recheck for hot connections, controller, etc.?
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1996 CC-Gasser-WILD THING
Lift, BearClaw's w/22's
Fender flairs, Diamond rockers
670cc V-Twin, HS gears