Have you tried replacing the intake manifold gaskets? I had to do this to my 00 Trooper (Nat. Asp.). It had problems similar to what you describe until I replaced them myself. No dealer had been able to find the problem; symptoms (since brand new!) included surging, stalling (that's right)! Rough idle, no power when cold. Anyway, the thermostat went out, and since it's under the intake, it was easiest to remove the intake manifold and I replaced the gaskets while I was in there.

The guys at St. Charles Isuzu says the problem is notorious on all 3.2 and 3.5's.

Keep in mind in order to install the supercharger, four of the bolts holding the intake gaskets tight need to be removed and reinstalled. The actual installation of the supercharger may have caused the gaskets to leak.

Nate