Single Mom needs tips

In June, I replaced the engine (new factory engine and supercharger) in my 2000 Grand Prix GTP (3.8) and had the transmission rebuilt because it was the trans (3rd gear was blown out) that led to the blown engine. When I got the car back, I noticed that when the car accellerated usually between 38 - 45 that the car bogged and the check engine soon light came on. The code for this was P0401 Insufficient flow EGR and Injector 3. I had the EGR replaced and the same thing happened again--same code. The car will drive fine one minute with no bogging and sluggish another, almost as if something is sticking and then unsticks. Last night the bogging was so severe in all speeds that you can press the accellerator and have extremely slow accelleration and the car shakes--it even sounds like its putting. Does anyone have any idea what I should start checking now?

Thanks so much

I'd look into the #3 injector, as it would cause a bog if one cylinder wasn't getting fuel.