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Mark, from what I have read the alternator will run hot at anytime. The issue is how the heat affects the rectifier /diodes in the rectifier. I am thinking our under bonnet temps exceed the operating temps of the alternator electronics and hence they crap out - heat equals resistance. Not having a big arse fan to cool the alternator will not be helping. I run a 3" marine blower to cool my alternators when it gets hot. At the end of the day you want your electronic controls as cool as possible - remember the diode expansion module i told you about?
If you send the current across 18 diodes instead of 6 they are individually doing less 'unit work' hence they heat up less from the electrical load. this does not have anything to do with the actual under bonnet load from the temps, but it gives your alternator more capability to generate at max current if the individual units are cooler - does this make sense?