Sounds like your TV cable is way out of adjustment - way too much line pressure. It shouldn't be shifting that early into 3rd. Check where the TV cable attaches to the throttle body linkage and make sure there's nothing wrong with the connection there (I know on Panther cars they had a problem with a plastic connector bushing getting brittle and falling apart, causing problems - there's a Ford part, a brass bushing, that is a permanent fix for this issue). Make sure that nothing is obstructing the TB linkage or TV cable's movement - vacuum lines, electrical connectors, etc.
Also check a few inches back where the TV cable sheath is held in place by a bracket to make sure the whole cable isn't moving or hasn't come loose and gotten hung up on something in such a way that it's causing it to be out of adjustment.
If all this is in order, then search for "TV cable adjustment" and read up on how to correctly adjust your throttle valve cable so that you don't have too much or too little line pressure. It's possible during the valve body swap that the TV cable was improperly adjusted, or not adjusted at all after removal and reinstallation. A poorly adjusted TV cable can burn up a perfectly good transmission in a VERY short amount of time. I would avoid driving the car AT ALL until you're sure you have the issue worked out.