Here it is-

 

The SRT places the air flow meter element in a LARGER area pipe. So, the signal it "sends" to the the ECU is that there is much LESS airflow than in reality. This in turn causes the ECU to reduce fuel relative to the signal AND the other imputs (throttle position, manifold absolute pressure, air temp, load, etc) I am surprised the car ran decently. That said it would be inadvisable to run the car under load without tuning. I am not sure what will work with the 3rd gen ECU but assuming the Neo or something like it will work properly get it to a dyno tuner and make CERTAIN your A/F ratios are within range. This should stop your CEL light problem and optimize the potential the larger capacity MAF and piping create.

Also interested in the use of headers on a 3rd gen. Anyone heard of this being tried? Anyone have the ability to check factory part numbers? Do the 2nd gen and 3rd gen share the same exhaust manifolds? The S&S will physically bolt to the engine but without some additional information there is no way to be sure of any other fitment. If they fit there should be a sizeable performance gain without any need for tuning.

 

MIke did you ever get the wiring diagram for your car?
Did you get a wire harness from Boomslang to hook up your Neo? I did thought they only Lexus they made was for the IS300.?