96 SL2 Jerking on acceleration

I have a 1996 Saturn SL2, with 164000 miles. Recently a new engine was put it with 60000 miles. I first start the car up and it runs fine, but once it hits the first 1/4 line on the coolant temp, the problem starts. Seems like it starts once I go into closed loop. Anytime I tap on the accelerator it jerks or bogs down then goes. Never does it when the car is cold tho, but once warmed up, does it every time. The problem doesnt happen when im in the rpm range of 3500+. But anything under 3500 it will jerk. Replaced TPS recently, and replaced O2 sensor before cat recently. Pulled the old plugs and have replaced, and the old plugs were full of white powder. Ive been told by a mechanic that the car is running very lean, and could be causing the jerk, because the car is starving for fuel on acceleration. But once after the jerk it accels fine, until I let off accelerator and depress it again.