Being a 96 with a backfire, I've got to say regulator/rectifier. I know you changed it but I'd unhook the red wire to it if it runs the same way when you get the motor back in.
Removed it entirely way back when this first started with no change
Also checked dor AC/DC voltage/ ripple/ freequency while having the problem and it was all clean at the mpem and battery with rhe RR connected.
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