OK I went back to the arena where that leader of the brotherhood was still laying there. I used the console to resurrect him. He stood up, all his clothes reappeared on him, then he became near invisible and walked out of the building. I don't know if he'll just start off where he's supposed to or what.
Jaffre still doesn't see Martin standing right next to me, but that's all so far. I guess the main mission is scrapped for me. I may install the game on another computer so I can play the main mission and not get confused on what saves I have to keep. I completed all the recommendations and am nnow totally in the guild.
I'm a level 17 and just don't want to lose all that work just to play the main mission