Abrupt hesitation after slight acceleration
 

Tahoe 98 4WD with brand new crate engine, new injectors, spark plugs and wires, fuel pump and filter. Engine runs fine in Idle, accelerates like a champ, but when very minimal acceleration is applied, or during a small hill, the engine seems to hit a bump after 20 to 30 seconds of applying a load on the engine. It is a very abrupt hesitation. After the hesitation, it works fine for another 30 secs until it hits the "wall" again. Seems like the load creates some pressure somewhere that is released? Or the load creates some blockage? There are no mechanical noises. May be electrical issues? Tranny issues?
I also checked the cat for pressure differential upstream and downstream and found no issues there (drilled holes before and after the cat and used a gauge). I left the holes (1/4 dia) before the cat and ran the engine and the problem still there.
The problem was not there before I replaced the engine. So I either screwed up during install, or one of the replaced components is bad? The funny thing is that the gas mileage is great now...

Any guesses?