Hesitation/Stumble on accelleration

[GWS]

Can you guys help me with the differential diagnosis of this new prob? Just had a rebuilt DTT transmission installed in my truck. The vehicle has been immobile for weeks awaiting the repair. Now that I've got gears, I am regulary troubled with a hesitation/stumble when accelerating from a stop. Check engine light is on as well. I will check the VA, drain some fuel from the filter, check the PE connections to fuel pump and MAP sensor, check trans fluid level. Failing this, I guess I should change the fuel filter and check pump pressures. Has anyone else had performance problems after the vehicle has sat for a while? Idle seems smooth, and power is fine when cruising. The problem seems to be only when starting from a stop.