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This is the output from the R/R. The three pin burnt connector is the in from the alternator.
The three yellow wires take current from the alternator, convert it and the four wires (2 black, 2 red) feed the current to the battery via the wiring harness.
 

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Read my post again. The r/r has two plugs. A three pin for power in from the alternator and a four pin to the harness. BOTH MUST BE CONNECTED.
 

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Or just cut the connectors off, then solder and heat shrink the wires. The regulator works just fine? Yes? Then there is no need to replace it. The issue is the gauge of the wires from the alternator to the alternator RR. This has been covered quite well over the last 2 decades. Solutions abound with the search function.

When soldering, it does not matter which of the 3 wires are mated to the other 3.
 

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the 1998 my bikes with the single phase alt and shendengan reg pretty much all burnt that connector out. with the 3 phase and 3 wires/terminals it's generally ok, with the single phase it's not. replace it with a good bullet terminal and it'll be fine.

re-reading it you've fitted a mosfet reg with red and black direct to the battery? just ignore the 4 pin. the reds will be hot, but if you remove the maxifuse from the maxifuse holder (front of the battery box? not sure on usa spec models) that'll kill the power to them.
 

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I put a mosfet on my 996 and ran the black / red wires directly to the battery. works great as I had a parasitic drain in the wiring harness somewhere. Battery holds a charge fantastic now.
 
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