UPDATE!
After waiting a week and not hearing anything from the shop I took the SEL to, I called. Seems the company that refurbishes the ABS module needed a part for the module they did not have. When questioning the general manager as to why he did not call me, I could hear him shrugging his shoulders. He then suggested just getting used one and putting it in rather than wait on the refurbished one. I reminded him that a new one needs to be uploaded from the existing module. He again mentioned that he never has to do it with any foreign cars. I called the Ford Dealer and confirmed what I already knew regarding uploading a new module. I also asked about the cost a the dealer. $489.00 for the module and $180.00 to upload and install.
I picked up the old module today and was charged $141.00 for the original removal of the module plus two overnight shipment via Fed-X.
I have learned two important lessons from this experience.
1. My old repair shop was trying to gouge me for $1200.

2. The second shop didn't know diddly about Ford ABS Modules

3. Always check with the dealer...sometimes they can be very competitive with their repair costs.
Windstar goes in Wed to have the new module installed and uploaded.