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Hardwyre, sorry I took so long to see this. I don't have the GM alternator swap, I went with a 1979 ZX alternator. Unfortunately it was a reman from Schucks and it died after about 9 months. But until then, no problems. Now I have an internally regulated 1978 Z alt and it it is working fine, it's actually stronger than the Schucks reman.
Your problem sounds more like an alternator issue. With the internally regulated alternator there is essentially nothing on the car that should affect it. The alt pumps out amps, the S wire tells the alt where to hold the voltage and the L wire tells you via the Lamp whether or not the alt is putting out more voltage than the battery. If you went with a one-wire, its' even simpler although I think that you lose the lamp indicator.
Alternators in general are susceptible to over-heating. Maybe yours is on its last legs.