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No. I have used an S4 alternator on a first gen for years they are pretty much identical just a few amps more capacity.
It has to be something really simple wrong with the car, you have put so much time in it and had it running it is time to go over the basics the car is still basically a GSLSE the engine core doesn't really matter and the manifolds are just moving air the fuel and ignition system doesn't know any different. is everything grounded really well?
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1976 Cosmo needing lots of work
1993 Rx-7 410 RWHP single turbo toy
1985 Rx-7 toy/project car 411HP stoplight terror
2001 Dodge ram 4wd.parts hauler
2016 Ram 2500 cause its a hemi
2006 VW TDI commuter
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I guarantee there's a pregnant redneck teenager somewhere in a shitty trailer park that thinks "Ebola would be a lovely name for their child"... 
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