1994 BMW 540i Transmission Program

I recently had my engine replaced. Prior to that my transmission program light would come on very rarely, usually when the temp was cold. The car would be stuck in 4th or 5th gear. I would shut the ignition off. Wait a moment and than turn the car on and than all would be fine. After the engine replacement this occurs all the time whether it is hot or cold outside. If I am taking off from a rather level surface there doesn't seem to be a problem. But if the car has to downshift frequently the light goes on and the car remains in 4th or 5th gear until I stop and turn off the ignition and wait a moment etc. The car also seems to be shifting more noticably (rough). The mechanic that replaced the engine said that because the prior engine had little torq the new engine may be placing more stress on the trans and thats why its happening more frequently. I replaced the engine because I truely love this car. What is your advise on the fix and is it really worth it $$$? Also after engine replacement the coolant warning light comes on - the temp guage does not move from center and there is plenty of coolant in the resevoir.
Please help - I appreciate your help and expertise in these matters.