I went ahead and installed the Magnaflow 3" cat. It does make a significant increase in performance, but I do warn you that the truck is a lot louder. Hopefully, with Gadget's new exhaust coming out this can be resolved. I have not noticed any decrease in performance in the low range and my boost is the same at WOT (around 8lbs). Note that this is with the TRD headers and exhaust

-2000 4runner Limited
Supercharger and all the mods