runs rough

Greetings all. I have been plagued by a yet-to-be-determined problem with my '02 ZX6R. Basics: 19500 miles, bought used with ~3800 miles(?) Previous owner replaced to stock jets with larger interior jets (sorry, don't know the sizes) I live in Minnesota, so I can only ride 3-5 months out of...

So I bought a 2006 zx6r recently for a steal. Everything works fine on it except for when I put the bike in gear and start moving the engine sounds shaky. I got it straight piped and with no power commander or anything. I thought that might be the issues but it idles just fine and can be revved...