Wagon power surge

My 1994 wagon is in the transmission shop as I type this. They were able to complete the rebuild. However now there is a "power surge". It's as though one min it is getting the proper amout of fuel and the next min it isn't. The transmission shop believes that there is a short in the transmission wiring. However i'm wondering if that is the case. Could it be the intertia switch, Fuel pump, or the ecm?

Is there any condition that seems to cause the surge to be more pronounced such as only after the engine is warm, only when it's damp outside, only when the ambient temp is below x degrees, shortly after hitting a bump or pothole, etc.? Did the shop check the fuel pressure? Was this issue possibly there before you took the car to the transmission shop but masked by other issues?

-Rod

No, I don't think it's the transmission. It's maybe a vacuum leak in engine, fuel pressure regulator problem, restricted fuel injector, or engine control system (egr, maf, O2 sensor...).