I have an older 15KW Generac Guardian that has no power output.  The model is a 0043903 and the serial number is 4239336.  For testing purposes I am running on LP; the unit wil eventually be run on natural gas.

I have a factory service manual and have been following the steps in troubleshootng the no output problem, and have concluded that the voltage regulator has gone bad and have ordered the newer finned one to replace it.

Whilst performing test 9, being led there from the results to test 4, however, I found that when testing the wires from the brushes to the #2 connecter, the '0' wire which should have led from the forward negative slip ring to pin 9, actually connected with pin 10, and that the '4' wire, which should have led to pin 10, actually connected to pin 9.  In other words, they were switched.

My question is, does this matter?

With some trepidation I hooked it up as described in the manual, 0 to 9, and 4 to 10, and tried again.  Same result, engine started immediately and shutdown after sensing no voltage.  

So I continued testing in order and found in test 6 that there were 10.1 volts field boost, indicating that the voltage regulator was defective.

I am not new to repairing things, and it really looked to me like this generator had never been disassembled, at least not that far (there was evidence that someone had tested at least some of the circuits in the control panel), i.e. it was wired like that from the factory.

So I am at a loss.  Do I run it with the new regulator as I found it or as I've rewired it according to the manual?

Any light anyone can shed on this is very much appreciated.

 Thanks,  Jim
Did you do a fixed excitation test appling battery voltage to the #4 wire and checking the output to the breaker and the 2 & 162 wires from the DPE winding?  To answer your question it doesn't really matter but the #4 wire is always closest to the bearing and the #0 wire closest to the rotor winding.   
I had a 15k gen, old style air cooled that gave me a fit. Stopped on red light rpm sense loss.  Red light on VR not glowing when running.  New VR no better. Cleaned brushes, fine for two cycles. Same issue.  Finally added the Up Fit Field Boost kit.  Been running for months now. Might look at that if you still have a problem.