A lot to cover here and I can't get to it all at once.
The TPS has a switch inside (IDL) which is used to help the ECU know when to run the ISCV (Idle Speed Control Valve). If it's not properly calibrated or the switch is damaged idle will be erratic and/or low. It's the first thing I'd check.
See here for details on properly calibrating the TPS. See here for testing info on the ISCV. It's unlikely that someone whould have removed the ISCV but it does happen in which case you need to add a tunable air inlet (some people use the throttle stop or misuse the dashpot or drill a small hole in the throttle plate (NOT recommended) or add a needle valve with filter to a vacuum line that's after the throttle plate).... The argument is that it's for simplicity. EDIT: I forgot that we were talking about a MKIII for a minute there. Any alternative idle control would need to source its air from in front of the throttle plate and bring it back in behind the throttle plate.
I wouldn't have deleted the EGR.... Especially not on an endurance vehicle. You lose the benefit of enhanced cylinder cooling when at part throttle and it's off when throttle is 65 or 70% or higher. But that's your call. If the VSV with the cut wires is back by the #5 and #6 cylinders it's either for the ACIS system or for the EGR (the wire color codes are for the EGR VSV)... Either way you should remove it completely if you don't want it and cap the vacuum lines or you may have a vacuum leak there.