I have never done it and am new to the Rocket and TuneEcu But take a look at the links below...
Tasks
which leads to here...
TuneECU TPS and ISC Stepper Adjustment - Triumph Forum: Triumph Rat Motorcycle Forums
Before you do anything with TuneEcu read the manual and then make a copy of the tune that is loaded on the bike currently. You can later compare that tune to the stock tune.
Different years are different tunes and apparently different ecu's.
If the secondary throttle plates have been removed and the tune has not been adjusted for that it seems there is the potential for the bike running lean. The power commander was probably used to adjust the mixture in these areas. The power commander install may have included a cable plug to fool the ecu into thinking the o2 sensor was there and working.
Do you have the o2 sensor to reinstall?
Rick