power commander 3

New to the site and just purchased a 01 929 a week ago, well its been cold and I really don't know how much this effects the bikes. Well it fires right up and it idles fine, its just that its got this stutter down low, like right off idle to maybe 1/8 throttle, after that it raps out fine. This could be because of not getting it to a high enough temp, 180 is about as high as it got just warming it up idling. It has the pc3 on it, and I was going to change plugs out just because I know nothing about this bike. My question is... can I just unhook the pc3 and hook stock connections back up without doing anything else? Im not sure about losing the settings it has now if I do so. I know nothing about pc3s or tuning them, any help would be greatly appreciated. It has a D&D slipon, not sure about breather yet, just havn't had time to check it out yet. I have a laptop I could hook up to it, does it take a regular usb cable? If the plugs do not fix the stutter and the air filter is clean I was thinking of unhooking the pc3 temporarily to see if that would help. Any suggestions for a newb?