Jeremy,
This might confuse you more. If your rig had a FIELD and ARM wire, which you taped off, it probably had a BATT wire too. You can attach the large BATT wire FROM the alternator to the BATT wire that was on the old voltage regulator. This will supply power to the system through the old ammeter, just like the generator did.
You can connect the larger wire coming from the DA plug, should be marked #2...maybe the red wire, to the big BATT lug right next to it on the alternator.
The brown wire should be marked #1 and it needs to connect to a switched voltage that is ON with the key when the rig is running. If the ACC position of the key is ON when the rig is running then it sure fits the bill.
I hope this makes it more clear.
Stuart
