Every spark plug NEEDS TO BE GAPPED CORRECTLY SOMEWHERE BETWEEN THE BOX, AND THE SPARK PLUG HOLE. No exceptions,, if you do not do this,, sell what tools you have, never get near the bike again with tools,,, and find a mechanic.

 

Like Terry said, try to do the job right or you won't learn what your chasing. Is this fuel injected? There were injector wiring problems around that year too.

 

Is the roughness mostly at idle then smooths out on acceleration? If so it could be the IAC needs cleaning. Idle Air Control.
This assumes you have a fuel injected motor.

 

Is the roughness mostly at idle then smooths out on acceleration?

Some sort of vacuum leak on the intake side. Compliance fittings, loose MAP sensor, Look for how to check for vacuum leak on intake side.

 

crappy gas?? too....a mechanic needs to find you

 

Didn't the 06's have 8 degree injectors, which were problematic. When they switched over to the 25 degree injectors it made a big difference.

 

Connector was loose, tightened and replaced, ran fine a day. This makes no sense. Then you changed plugs and still runs rough. If it ran fine for a day on the old plugs something other than the plugs is going on me thinks...

 

Connector was loose...for how long? {And why was it loose?} It may have damaged something upstream, any codes show up?

 

Are the wires touching each other? Old wires can short out against each other, or arc and cause rough running etc. (they don't have to be touching each other for this to happen or be the cause)

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I'd check fuel filter!! Highly neglected,, before digging to deeply,,