Stormrider
Something is not correct, and I doubt that it's your Baro sensor. Sorry, I don't have TuneBoy on the Mac Notebook I travel with, so have to do this from memory...
Follow the instructions in R3 manual for replacing TPS exactly, except use TB instead of Triumph tool. The TPS does not go completely in one direction to install... the initial voltage reading must be set correctly. Also, you must ensure throttle plates are completely closed and reset ISV as described in manual. It is doubtful that you have another bad Throttle Position Sensor.
Hope this helps.
hombre