to add to Flux's comments
and i too have lost track of what all you have done with the alternator, but
first things first
i seem to remember you haveing a oscope
you might want to take a look at the output waveform on the scope
if you have a bad diode i would expect a bad blip periodically on the waveform?
if you feel you must open the bugger up
remove the front half of the housing leaving the stator in the back half
the remove the stator from the rear half, it is retained by 3/8" hex nuts, on 3/16 or #10 studs that pass thru to the outside that make the AC posts. remove the inside nuts and lift out the stator.
look over the stator well, i don't expect any problem with it, but look it over just the same.
the rectifier bridge has all the diodes welded in jumpers making seperation near impossible, so you can only check one side of the other, and not isolate a specific bad diode.
they are press in .500 diode, i use 570 and 572's which are 70amp and 200piv rated units standard high power silicone fast recovery,, the oem's are using avalanche diodes that clamp at about 30vdc.
usually if you test the AC posts, 1-2, 2-3, 1-3 and all the voltages are the same
the diodes are likely just fine.
too bad you don't live closer, hard to diagnose problems online
if after all this you find bad diodes, either limit the output current to no more than 100amps continuous or get the thing mounted so the fan turns the right way, or
get a reverse rotation fan... and then limit it to 120amps continuous.
and then only if you are spinning it upwards of 4krpm
lastly if the machine has been damaged due to overheating, forget the darned reostat control, you have no way of knowing what is happening with a reostat unless
you are sitting in front of the ampmeter with the dial in your fingers, walk away
and anything can happen. someone throws a load on the batterys, and your 100amp
setting of the reostat not becomes 140 or max output for the alternator,,, how long
that load stay's on is anyones guess, and certain overheat is the result.
far better to use the oem regulator until you get your controller working or buy a suitable controller that has an alternator stator/case temp sensor to protect the alternator.
bob g