Ok - start by separating two very different things that you might ask mechanics to do (or that you might figure out how to do yourself). One thing is maintenance. Just on mileage and time you should absolutely get a new fuel filter and at least have someone pull and check the plugs. Odds are that you need new plugs too. These things are not done to "repair" problems but are normal things that need to be done as a matter of course just to properly maintain a piece of machinery.
The second kind of thing is "repair" - as in when something breaks - like maybe some part of your TCC lock up system gets out of whack.
Anyway, when your car is in gear the engine is under more load then when it is in park and neutral. If the car is only marginally running to begin with, putting it in gear can make it run rough or stall just b/c of simple maintenance things - like a weak spark or low fuel pressure from a clogged fuel filter. So you really want to make sure none of that is going on, but more to the point you want to do that even if it doesn't "fix" your problem. These maintenance items are not actually "fixes" (repairs) - they're just maintenance.
Anyway, if all of that gets to be in order you should make sure that you don't have any vacuum leaks, that your idle air control valve is cleaned and checked along with your throttle body. You might also get some specifics from the transmission shop about how they reached their conclusions.