I would first check to see if the generator would motor. Remove the Fun projects regulator for this and any other tests. Remove the fan belt and touch a hot wire to the post that comes out of the generator. If the generator begins to turn like an electric motor and is turning in the correct direction it is probably OK. If not or it motors in the wrong direction you probably made some mistakes when you installed the field coils . if the generator motors backwards you have the wrong wire grounded that comes off the field coils. If it passed the test, put the old cut out back on and hook the wire back to the cut out. To polarize , without the engine running touch a wire from one post to the other of the cut out for a couple of seconds as Tom Wesenberg said and the generator will be polarized and this won't hurt the old cut out. I know what I am talking about because I have ran 12 volts with a reproduction cut out, the only thing is with a cut out you won't have voltage regulation. If you jumped a wire across the posts of the Fun projects regulator you have probably killed it.
Actually you DON'T need the 12 volt field coils to run 12 volt. This was told to me by John Regan himself. The main difference in the field coils is, the 12 volt coils have smaller but more wire. I believe that larger wire is better. and the 12 volt field coils are more difficult to install because more wire is harder to squeeze down so that the armature doesn't hit the sole plates.
As far as the wiring I used the original wireing harnesses. The model As that I run with mallory dual point distributors , I run a wire from the distributor to the ignition switch just as you would with a repro switch and cable. You can look at the wiring diagrams in Brattons catalog and the only changes you will need to run negative ground is reverse the connections on the battery, coil and the ammeter. I think that most if not all the repro ammeters are model T and are negative ground. If it doesn't show a charge try reverseing the wires on the ammeter. You can hook the electric fuel pump to the ignition switch or you could just run a hot wire with a toggle switch between the wire and the pump.
I have been running the Fun projects regulator, 12 volt positive ground for four years with NO problems. I hope this will help.