Has it run bad from the time you got it back from having the transmission replaced? If so, first talk to the guy that did the work and see if he will help make it right. More than likely there is wiring that got disconnected or moved when the transmission was being worked on, causing your issues. I know when my Escort had work done we missed the O2 sensor at the cat and I had a CEL light and engine ran rough. If he's reputable he should help without charging you, as long as it ran right before he worked on it.
If you are getting a CEl, find out what the codes are and post back. You can have them scanned at a car parts place, usually for free, or need be there is a how-to for reading them throught the odometer display.