i will take that bet that you are never gonna get a dealership to work on your car for nothing..........
if they think its the alternator then they will replace it and maybe later found out that they screwed up and forgot to connect something and then that that mystery wire back and then tell you yes its the alternator....and who is gonna prove them wrong and even if you do then who you gonna complain to??? Ford, they dont care about the work of a dealership... as long as the delealer does the warranty work that ford has to do to cover its a$$ thats all they will do is take car of the warranty stuff.... the alternator does not have anyting to do with the warranty.. the bad wiring harness is like mine.. the a/c unit blew due to wires shorting out on the high pressure cut off switch...
No they would not cover it... i had to do it myself and make sure it was done correctly... i then used some liquid tape, a liquid plast/rubber that you paint on the wires to keep them insulated.... i hope i never have to bring this car into ford to have the harness replaced.. the mechanics dont get enough time to do the job correctly and ford pays for about Six hours of labor for this 12 hour job........
most mechanics dont want to do it as they loose money doing the job....