Jeeps Canada - Jeep Forums - 4Cyl YJ issues, need suggestions

I just replaced the 4cyl in a 93YJ that had a toasted motor (huge hole in the block,broken piston).I bought it really cheap with the idea of swapping in a good motor. It still ran amazingly enough so I know that electrical, fuel pump etc (all systems that would remain on jeep while swapping the engine)were good. I was able to listen to the replacement engine before pulling it from the donor jeep. It ran well.
After the swap I am now getting a hesitation on the new motor. It sounds like a volkswagen bug. Intermittent. Loss of power. It would run good if I accelerated slowly but if I tried to accelerate at a normal rate it would sound like a volkswagen and would lack power, if I released the accelerator abit it would run smooth and you could feel the jeep lunge ahead at a normal rate of acceleration.
Wiring was hooked up correctly, fuel filter was changed, I read my haynes manual and it told me that you could only adjust the timing on the carbureted models. I've run two tanks of gas with injection cleaner and gas treatment but nothing has changed.
My next step is to check the distributor and spark plugs, any one have any other suggestions?