Being the tightwad that I am, I would buy that used powercommander 3 usb and then call powercommander tech line and ask them for the correct map for your bike. Installing a map in a pc3 is not hard, but takes a little reading on dynojet's website. With their canned map loaded your bike should run OK, if there is not a problem.
That should get you running OK for 165.00 and some of your time.
Another option is to buy the pcIII from fuel-moto with a map for your bike already installed.
http://www.fuelmotousa.com/fuelmotoefituner.htmThat gets you a map from a good tuner and their own branded pciii for 239.00 plus shipping and all you do is hook it up . And yoy get a new WARRANTED UNIT. So easy even a caveman can do it.
These options will not have your bike running to it's absolute potential, but will save you some bucks over having the bike tuned.
Kind of depends on just how much cash you want to sink into the bike right now. But these 2 options are pretty cheap and should get the bike running better.