I hesitate to add anything to what Hotrod has written, but I can write that I had the same problem that Chad is experiencing when I first got my truck. I had been persuaded to replace the original VR with a new one, and struggled with it for about a year. I did my best to make the adjustments by the book, but like many of us weekend wrenchers I do not have an ammeter that is needed to do the job right.
Particularly when the headlights had been on the contacts on the cutout relay would fuse themselves. I got used to watching the dashboard ammeter every time I shut the truck down, prepared to race to open up the VR and break the contacts.
Eventually I noticed that the old VR had two sets of contacts on the cutout relay while the new VR had only one set. Here is a picture of the new VR:
New voltage regulator The original style can be seen in the shop manual.
Finally I took out the new VR, sat the old one back in, and used the shop manual and the advice from the Stovebolters to get the old one working right again.
I for one am convinced that if you are using a newer VR with the single set of contacts on the cutout relay you will have a greater challenge getting it to work well.
Karl