[TitaniumTT]

Gotcha, If you had a switched 12v source connected to the L terminal, chances are it's probably cooked, sorry.

Here's the problem, you're going to have to modify the wiring significantly if you're going to use the chassis wiring (S4) with the S6 alternator and have the idiot light work correctly

Ok, so before you go digging into the harness looking for the mystery wires here's what I would do
Use that existing 12v key wire that you originally had running to the L terminal. Put a small resistor on that wire (I can tell you what I am using tomorrow night) and connect that to the L wire on the S6 Alternator. Yes I realize that this sounds alot like what I just said probably cooked your alt, here's the difference, look at the S6 charging diagram. You'll see the L wire runs to the alt via the ignition switch (so it only sees power when the key is on) through the idiot light in the dash (resistance) and through a diode (one way check valve). So by using that wire on the shock tower (which I'm assuming is B/W or B/Y), you can add a resistor to mimic the resistance of the 1.4W dash bulbs and that solves that problem. Now the S6 will think that your B/W or B/Y wire is being fed through a lamp circuit like it should be.

The S wire on your alt can be temporarily hooked up to the alt charging post or brought back to the battery, either will work fine for testing purposes.

There is a big difference in the way the S4 works from the S5/6. The two main differences are.

The S4 uses the R terminal to turn itself on, and to sense the voltage. The S5/6 uses the L terminal to turn itself on. The S4 doesn't have an S terminal, the S5/6 don't have the R terminal

The S4 uses the L terminal as an output. When the alt goes bad or isn't charging, this terminal latches to ground triggering the idiot light. The S5/6 use this terminal as a turn on. When it sees voltage, it excites the alt.

The S4 doesn't have an S terminal. It uses the R to determine voltage regulation duties. The S5/6 have the S terminal and they use this to sniff the voltage to determine regulation duties.

Does that make sense, at all? Again, this is what I went through 3 years ago