Sounds to me like you've found the source of the lack of power, now the question is; what else did the 'mechanic' screw up? I'd send the guy the pics and tell him that you still haven't found out why it died or what the noise is, but from the quality of work in evidence so far it's probably due to similar incompetence (you can include the pic of the blowgun that was left in the engine compartment if he questions you). I had my doubts about the mechanic's skill level when you said they installed a used lower intake plenum.

95 Montero SR
3.8 MIVEC, Advance headers, 2 1/2" exhaust, Magnaflow muffler, OME shocks & rear springs, 2" body lift, 3" tank lift, 4.90s, TRE front locker, factory rear locker, Roger Brown Rock Sliderz, 315/75r16 (35") tires, Sport big brakes