I am not sure what you mean by 99 and up alt being different.
I have a 2000 5.9 from a durango, and used the alt out of an earlier dakota and it worked fine. the alt is the same from like 96 to 02 if you look on line.

as for the vr, I am using a pre 70 single field vr on mine. no issues.
ground 1 wire and the other is wired to the vr like any dual field vr.

don't know of any mag engines using an internal regulated alt. they were all computer controled.