The irmcs are valves in the intake that stay closed.In 2001 they introdroduced the IMRC in the intake. There are little butterflies inside the intake and a module on the back of the intake to open and close the butterflies. At certain rpms they open up. These symptoms point to this culprit. Most 2000s do not have the wiring for irmcs. I know they were introduced in 2001. I am not sure if late 2000s have irmcs. You would have to pull the old intake and install it on the new motor or use clamps to keep the irmcs constantly open. If you look on the back of your old lower intake and see bare metal, you found the problem. I think it says 9j559 on the pic. It will look like black plastic and metal. The part near the back of the lower intake in the pic.
If you change comps the car will not start because PATS will not communicate properly.
new engine,1.7 rocker arms,Pipes exhaust, shorty cats , shorty headers,under drive and overdrive pulleys,4.2 upper plenum, throttle body spacer, cold air intake, stage one clutch, shorty shifter, and tune. 8.8 in storage