I hate to hear stories like this. I'm sure you searched and found many posters have gone through the same issue. Well, the issue being having tranny rebuilt and STILL having the same problem.
As many members will tell you, besides testing the voltage, they would have dropped the pan and visually checked the fluid and the filter. Perhaps throw in a partial fluid exchange at home.
I sincerely hope that your rebuild came with some sort of warranty. Go back to the shop and demand they stand behind their work. Was the work done at a chain shop?
You mentioned that the shop said something about the TC? Replacing a TC isnt that expensive compared to a rebuilding a tranny.
I know none of this helps you, but I would go back to the shop that rebuilt the tranny. Keeping going back until you get it done right.
I had my tranny rebuilt a year ago and it came with a 3yr/36,000 warranty.
**NOTE:
My tranny went into limp mode before it was rebuilt. Also, there weren't any CEL's, but I did have a stored code.