Some thoughts.

They lied when they said that they adjusted the idle -- in a '92 (LH2.4), there is no way for them to adjust the idle (nor the ignition timing, for that matter).

First, and most obvious (given that we're talking about a newly reworked transmission), can you feel (or do you have a dash tach to verify) that the transmission is shifting up through all the gears? Why do I have a feeling that your description might be indicative of a car being lugged from a start in too high a gear?

Alternatively, however, if you are perceptive and accurate in your description (and if all the gears are working, viz the preceding paragraph), the problem probably isn't with the transmission -- it sounds as if the engine just isn't responding to your throttle input. However, that isn't to say that they didn't cause some "collateral damage" to your fuel system in the course of repairing your transmission.

It's not likely your fuel pump, though, as problems with these usually are worst at higher speeds (when more fuel is needed), not low speeds.

Is there any idle irregularity? I'm thinking perhaps a bad AMM? And have you checked under the car near the transmission. Are the fuel lines good?

And finally, although it's almost unheard of in such a new car as a '92, high concentrations of alcohol or (in past years) MBTE could have prematurely broken down your transfer pump's hose, the 2 inch hose between your transfer pump and the metal fuel line. If you were accelerating up a hill with a half tank (or or less) of fuel, this could aerate your liquid fuel with bubbles and cause a fuel starvation problem. Maybe you managed to reach the top of the hill and leveled off, and that's when your car begins to "run like a champ" again?

Good luck. I just spent a month (and a lot of dollars and time and scraped knuckles) trying to figure out an emissions problem in my '84. It can be very frustrating.