Well what is your budget first of all? Have you priced out a built auto, converter, standalone controller and all the other misc stuff like pedals, yoke, kickdown cable, shifter etc... ?
Then IF the shop knows what they are doing (that is a big if) it's probably going to be another $1500-$3k.
You would obviously be able to make back some money from the T-56 you are removing. Probably in the $1500 range depending on mileage.
2000 Mustang GT Steeda build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.