It's been a long road, one that I don't want to soon travel again.
The new shop put in the New Motorcraft alternator and they say the lights no longer flicker and the charging system is stabilized. Absolutely music to my ears.
Total diagnostic and damage costs
Dealer electrical trouble shooting $104.86
Independent Shop Diagnostics $ 60.00
Independent Shop Diagnostics $125.00
New Battery (it fried the old one) $120.89
My portion of the original alternator $ 32.00
Total spent to diagnose a bad alternator $442.75

(This total doesn't even include the numerous hours I spent looking at it and driving it all over hell's half acre to get it looked at.)
The kicker is I made numerous trips to the shop where it came from and always got the same answer, "it's a short in your cars wiring, not our alternator".
All of this could have been avoided had they just put in what they claimed they were, which was a new Motorcraft 140amp alternator. So now the big question is do I have a legal case to recoup some of my losses should I decide to go to small claims court? I think I do, I have everything well documented. Not to mention they warranty company is investigating them for fraud now, not sure if I could get a statement from them but that would be great if I could. If you think about it I spent nearly as much on proving the alternator was bad as the warranty company paid for the new one.
What do you think? I'd like to hear your thoughts and suggestions. I am not sue happy, and have never sued anyone or business before but I seriously thinking about it this time.
Thanks,
Matt