Holy sweet Jesus, thats alot of money!!! If you can stand to do the alternator yourself, how much would that knock off the $1000 bill? Hell, I am sure its worth doing it yourself. I got my "new" (rebuilt) Motorcraft alternator for $180 +$75 core. IMHO, I personally feel that the Autozone/NAPA/O'Reily brands arent worth crap. I know someone that worked at O'Reily's and said he did so many warranties on alternators it was not even funny. And for $180 for the Motorcraft, or $160 for the NAPA rebuilt, I am going to spend the $20 more for Motorcraft. BTW, you should also do the belt if it is original while you are at it, so figure another $30 for that. While you have the car on a lift (I would not attempt the alternator any other way, its hard enough with a lift) you could get that O2 sensor out of the way for like $90. With all that out of the way, that would probably get rid of the CEL, I am assuming that is being caused by the O2 sensor and not the leaking seal. So with all that out of the way, you would only have Ford to do the UIM gasket, which if you look around, would probably not be all that hard to fix youself also. I personally would never take my car to Ford now that I am out of warranty. If there is something I cant do myself in my shop class with a 30+ year mechanic helping me, I would just bring it to a local shop. Ford will almost always bend you over so far you will be kissing your shoes. Just letting you know, I am here for any help you might need. Good luck, and PM me if you need any more help!
-Nick