The auto transmission has its own computer. The TCU is located on the tunnel behind the ECU. Limp mode could be being caused by something as simple as a blown fuse. Stealth316.com has a procedure for pulling trans codes. If it just simply blinks then you either have a faulty TCU or the fuse is blown.
As for the starting and shutting off my guess is the ecu rebuild screwed you. You may want to find another owner in the area who is willing to test your ecu in their car. Don't try theirs in yours because you could potentially damage their ecu. If their car acts like yours with your ecu then you found the problem.