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Just an update, sorry took so long to post the solution to this issue, but I had the alternator cable from the fuse box to the battery not hooked up on the B+ terminal. Which I figured out from the diagrams. But even then when I hooked it up, the alternator continued to over heat - and I still had the extra cable from the wiring harness which is not represented in the 96-97 service manual, nor other people's trucks that I looked at. I do not know why I have it, but it counts as a ground... As one can see from the diagram, and based on the size of the cable, who would ever expect this to be a ground?
Anyone able to explain this to me? Its running now.
Not the same wiring as mine Alternator Cable not Seen