Emu, if the bike is still under warranty, why not let the dealer have a go at it? were they not able to replicate the problem when testing?
the symptoms you describe - specially the fact that it runs like crap, you re-boot it and it's ok for a while, suggest a sensor... or something else that gets reset on the on/off cycle. bad ground somewhere, or maybe sticky 2nd-ary flies...(had that problem on a car, with simmilar symptoms). Do you have O2 sensors working? i really doubt it is PC, sure TuneECU is great -blah, blah, blah - not putting it down in any way, briliant piece of software and very usefull, but some here tend to try to find faults in PC just to justify swiching to TuneECU (just my opinion...). i've had 7 PC's (2, 3 and 3 usb) over last 10 years or so, never had one fail... never heard of one failing in our racing comminity, and almost everyone uses one... not saying it cannot happen, but i find it unlikely. Again, not putting down TuneECU, it's great, i use it, but i still have my PC, and i'm keeping it.
few suggestions:
sensors... all of them play a role in determining fuel injection and/or ignition rates, and are re-set on 'reboot':
MAP sensor
air temp sensor
ambient air pressure sensor
throttle valve sensor
2nd-ary throttle valve sensor
o2 sensors
other:
reg/rec - if you have a voltmeter, you can easily check it (procedure in the manual)
fuel pump/fuel pressure regulator - not sure how to check it, other than trying a new one...
fuel filter/line obstructed
2ndary flies stepper motor
air filter (unlikely unless O2 sensors enabled)
air leak around TB's
vacuum hoses (if you did not remove them)
SAS leak/failure (if still there...)
intermittent problems are a real pain, hope you get it - or at least can replicate it for the dealer, since you're still under warranty...
cheers!