Not knowing exactly what have and how the 12 volt conversion has been wired.
It would be better to let someone with a lot of experience in 12 volt conversions to advise you on how to proceed.
It is hard to advise someone on how to wire their truck unless you are there in person.

These guys would know where those wires go, at least they would ask the right questions.
Here is a link to YNZ Yesterdays Parts they build wiring harness.

The thing is, there are different types of alternators and each are wired differently.