I have ran into that exact same problem before, and then replacing the case fixed the problem, you may have just lost 3-4th from the first and then the new trans did the same from a tweeked trans case, either way good up to 550hp I would want to see in writting and what parts he put into it as well.
I had the exact same problem in our 2003 mustang.
You may want to use another trans shop.
What kind of convertor did you put into it and did you put a new one in with the new trans as most trans shops require that to be done as well.
Torque Converter Limted Time Only??????????
That part confuses me, did they send you a new one?
I am worried about the case are you sure they did not use yours like you received the new one and then shipped yours back to them as a core or did they require you to ship your old to them first?