I have that wire coming off the radiator support area which goes to the alternator, it isnt hot and has no juice, I had another random wire coming from the battery so I spliced that in to the line to give it power, but things still dont come on unless I route the alternator to the + on the starter, this may not be correct but if it charges I'll be fine with it, Im not sure what happened but it wasnt like this before I pulled the small block and I didnt change a thing. Any thoughts would be great...

There's a small junction block hiding behind the battery. Maybe something happened back there.

The battery is in the trunk, but I know what you mean... where it used to be. I'll check again, The way I have it now seems alright but it isnt pretty.