Regarding your power commander. Several questions. Was the bike running ok when you bought it? A power commander that is not set up properly will cause your bike to stall, sputter, hesitate, some deceleration popping is normal but it should not be misfiring. Secondly have you started messing with the buttons on the pcIII? It pays to do some research and reading before you start toying with electronics. The green led's are for your throttle. If you rev the bike up a few times you will see the led's go up and down depending on your throttle position. (ex. Half throttle, led should be around in the middle). If the bike was running ok what made you start toying with it?
Whoever told you about the lights being all green doesn't know what they're talking about or you interpreted wrong. Think of the green led as your rpm gauge but for your throttle position. You need to set up the powercommander with a computer not with those buttons.
If you want to check the unit out and have access to a laptop, i suggest visiting the power commander website,
http://www.powercommander.com/power...ntParts/powercommander_replacement_parts.aspx you can buy a usb cable and CD with the software for the unit for about eight dollars. Order the usb cable and cd. Install the software, plug your laptop into the bike via your powercommander and it will show you what map is installed. I'm sure the owner of the bike had this done previously but if the bike isn't running right 15-20$ isn't a bad investment. I would suggest if you haven't played with the buttons yet and the bike is running good then leave it.
Loading map's and playing around with the software is fairly easy if your ok on computers. If you feel comfortable doing this yourself then order the parts off that site, it's a good idea to have them or ask the fella that you bought the bike off if he still has them.