Well it did this same thing on the old motor,and this is a completely different swap,nothing from the old motor is on this one. Dyno inc was able to fix it when they tuned the car and adjusted my air fuels,thats why im thinking the fuel pump is causing something.

Edit:im going to buy a new harness,im thinking the plug for the engine temp. sensor is shorted somewhere it is throwing the air/fuels off when the engine is warm.

Btw a while back i removed all of the emission crap and the charchol canister.