With it being a new shop it's hard to tell. You MAY get lucky and they are doing a quality job but just selling it dirt cheap to get their name and reputation out there. Like PopRichie said I would ask about the Warranty How long/miles and if it's Parts & Labor (Make sure you get it in writing).
As for other questions, read up on the transmission.
http://www.explorerforum.com/forums/showthread.php?t=146956 is a great place to start. Read all 4 parts. The 5r55e is a new updated version of the A4LD. If you are mechanically inclined you might decide to rebuild it yourself after reading it. (I did, I'm still taking mine apart, it's a project truck so I'm in no hurry).
http://www.explorerforum.com/forums/showthread.php?t=146953 is another very informative thread. It gives some details about the 5R.
Try to find out what Technical Service Bulletins are out and what updates Ford did in the later years of production and ask the guys at the shop if those were done during the rebuild. I'm sure there are some threads here somewhere with information about them. Write down the specifics about what you find, so you don't forget or confuse something. For example: A TSB says to enlarge a particular hole in the bellhousing to allow for more fluid flow to a certain area (I made that up but it could be close to a real one).
I'm sure (after you've at least read the threads above) that if you posted questions that you think you should ask you would get some more responses. Changing the title might help to. Something like "Are these good questions to ask a Transmission shop?" might catch someones attention better.
I'm sorry I couldn't give you questions directly but I'm still in the learning phase myself (which is why I'm taking my time rebuilding my transmission). I hope you are lucky and that it is a good shop just working cheaply now to get their name out.
