If the Power Commander is jot functioning the bike will simply not start or run. It 'could' be a cable problem such that one or more injectors is not working.
If the TPS was flaky that will affect the PC, it gets its mapping feed from there.
If the previous owner was a dork or a tinkerer, they could have buggered the fuelling every 500 rpm all through the range.
It is as easy as 1, 2, 3 to put a zero map in the device and run the bike as standard.
1 Download the software - free and intuitive.
2 Connect pc to PC, copy current map (for wind-back and reference purposes).
3 Install a zero map. There's one in the software or on the website.
You can always go back to the copied map.
You can always get it 'properly' set up on a PC aware dyno.
The main dealer won't (and shouldn't) touch a PC.