66and06stangs

I have looked at several threads from a search for SJB. I just bought an 06 GT vert. The top won't work, found they rigged a pair of relays under the back seat, about burnt the car up with a jumper wire, took it to the dealership to get it put back to stock, THE DEALERSHIP GAVE UP ON ME, so I'm trying to figure out what to do. I found a service manual online (that I bought) which says the whole system is controlled by a thing called a Smart Junction Box. It also mentions that it needs to be programmed... I'm going to call the dealership today to find out exactly why they bailed on fixing the car, when i picked it up they mentioned a discontinued part.
So, I searched online and I see these available on the 'net... what programming needs to be done? If it is just the keyfobs, that is insignificant to me, I just reprogrammed 2 new ones after buying the car. What is the mystery that would make a Ford dealership just give up on it? They didn't even charge me the fee for dropping it off - the guy said no charge, just come get it......