I would not suggest running without a thermostat. BUT you can drill a tiny hole
through the brass plate
(avoiding the bellows) so that air can escape if there is a bubble. If it did get hot and the thermostat is
any good at all it should have opened and allowed the bubble to come out. Also since it cooled with
the electric fan it is hard to believe there is a bubble. I'd recommend about 10° more ignition advance,
or wherever it idles the fastest. (Usually comes out about 20° on mine and it runs cooler there.)
You may have to adjust the idle back slower when you do this to keep it reasonable.
I notice a blue hose coming from the head where a FI engine would have the auxiliary air regulator -
Where does that go? Could it be bypassing the cooling system (like taking out the thermostat does)?

You have to have the regulator that matches your alternator. If you have SEV/Marchal/Motorola, you gotta use
a regulator made for them. One made for Bosch alternators will not work satisfactorily, period.
This could be part of your problem. If you can open the regulator you can check to see if the points
in it (if any) are clean and not welded together. Also you should check the voltage and see if it is
charging and how much. If the voltage is low (13v, for example) you may be able to adjust it by tightening
the spring on the points that are spring-loaded. This is an unathorized repair but it has gotten me by for
several years in places where parts were hard to find.
--
George Downs, Bartlesville, Heart of the USA!