First off I fully believe in the power commander setup and its obvious tuning capabilities.
There is an inherrant problem with the autotune, its like cruise control for air/fuel ratios, in saying that does anyone here drive down the road on cruise control without watching what they are doing, other vehicles, animals on the road, icy conditions etc etc.
By letting the autotune only monitor air/fuel you are not alowing the ecu to protect the motor. If all it is interested in is air/fuel, it will fight the ECU when its trying to protect the motor, the ECU richens the mixture then the autotune leans it to maintain a specified a/f mixture. So say you get detonation due to bad fuel, the deto sensor and pipe temp sensor monitor this, the ecu decides to add fuel/back off timing to cool the combustion chamber all the while the autotune is fighting to maintain its holy grail A/F, and you have a blown engine. Add to that the fact that anyone in the automotive world knows about O2 sensors and how much they like oil or anything else on them and god forbid you run leaded fuel which kills their accuracy over time as well because anything in the path of the exhaust gets a small coating of lead.
The bottom line is buy the autotune/PCV combo, it works well, and go like this:
1) do your mods
2) upload dynotechs closest map for what you have
3)richen those numbers for safety
4)ensure you have good quality fuel from the same place you always buy
5)go for a ride
6)once you have verrified that the ECU is ok with your mods (no deto, CELs) activate the autotune
7)Ride around without doing long pulls to allow the autotune to start building a map, get progressively more aggressive and make sure you cover all your riding types, full pulls, 6500RPM powder floating, 8000 down the trail under little load, basically let it see how you ride.
8)monitor everything you can, piston wash, oil consumption, coolant temps, EGTs, remember the autotune doesn't even care if you are overheating.
9) once you feel that your sled runs as you would like it to save your map and de-activate the autotune.
10) Pull your expensive O2 sensor and replace it with a plug, check all the PCV connections. Ride it, make sure everything is good to go, then enjoy your mods. Now the ECU is protecting your unwarrantied ($3000) motor and not having to fight your $300 autotune. Then let your buddies use your autotune for $50 a shot, let it pay for itself.
As for anyone worried about your voltage regulator take a few minutes and check your tailight wiring harness, it likes to short out on the tunnel taking out multiple VRs over time, finally killing the ECU due to undervoltage. Another area that I have seen is at the handwarmers, if you happen to twist your brake or throttle or added a left hand throttle or rolled the sled, just check over the wiring especially where it joins on to the warmer itself. Polaris wiring and electrical are pretty lackluster but mainly in routing and wire selection. The VR is not the problem, its just what happens to get taken out by the problem.