So, I followed the attached diagram (with the execption of jumping the "S" wire straight to "B" without a fuse) and have searched but couldn't find anything.

The "B" terminal get's extremely hot when the plug with "S" and "L" is plugged in. So much so that it has rusted the bolt and is melting the insulation off the "B" wire.

I metered the battery with the "S and "L" plug unplugged and got ~11.8v and it would go up and down with the rpm. I plug it in and it stayed constant at ~13.6v no matter what the rpm is. So, it's not the regulator.

Is this the way it is or ???

Also my battery tends to go dead with the "S"and "L" plug plugged in.

 

Well it may help if you inform us as to what series of engine or car you are putting the S6 or FD alternator on!
I know that on an S4 car wiring,One of the harness wires are NOT used.You simply Cut it.and tape it out of the way.

 

It's an s4 t2 motor.