I bought a used 2011 TXC250 and it does have a power commander V on it. It has a bog on the bottom and its especially bad when the engines cold. I do not really know what I'm doing but I was thinking about installing the auto tune. I assuming I can just install the auto tune then hook my laptop up to the power commander and turn on the auto tune correct since the bike runs great minus the small bog on bottom.
Yes you can. You can also tell the autotune not to work in certain areas by putting 0 in the target A/F ratio. When zero it doesn't do anything. I had great results with autotune if setup correctly, the only region it doesn't work very well is in low rpm- low throttle specially on one cyl engines. This is due to the pulses in the exhaust and might be a problem for you as that's the area you want to work in.
Drain coolant and replace. BTW, you don't need to buy the auto tune. Once you get the temp sensor sorted, call ZipTy racing and ask for Michael. Also, go to this thread and read on. Check your current map against what's listed and go from there. http://www.cafehusky.com/threads/zipty-husqvarna-factory-powercommander-5-race-maps.33459/
Autontune works well on my 310 but you can still just tune it manually depending on what the bike is doing and what throttle position and rpms. Download the software from dynojet and then plug into your pcv to your computer and get map and makes some changes and send back to the PCV. The cells are all percentage changes so go positive or negative a digit or two depending on whether you feel it's rich or lean. Test it and adjust as needed. The autotune in any case requires an 18mm bung weklded to your header. I think if just a slight bog, you could "re-jet" in short order w/o autotune. May just be a lean spot.