Here is a response from the MUD forum:
That is a pretty wide question.
The snorkel could be part of it, the factory intake brings in a lot of hot air. With forced induction this could lead to detonation and resulting ignition timing retardation by the ECU, try premium gas, but the hot air still reduces the density of the intake charge even if you are not pinging.
The exhaust could be another, aftermarket exhaust can help or hurt depending on design and what the motor needs, main effect is velocity out of the exhaust port ands its effects on scavenging. Generally cat back systems do not have much of an effect either way.
I do not know specifically how reliable the TRD supercharger is but in general superchargers can develop seal problems where the pressure they produce is reduced.
could also just be LC#1 has engine troubles, overheating, carbon on the pistons, low compression, uneven flow in the injectors, out of spec valve lash, bad timing, poor valve seat, vacuum leaks, exhaust leaks that bring in air before the O2 sensor, etc etc
'97 40th Anniversary, OME 2.5" with 35's, ARB bumper & lockers, Warn M12, ICOM radio, CB, dual batteries, auxillary gas tank, etc and now a snorkel