Pretty sure it's one of two things,
a) Like already mentioned above, a badly seated throttle cable.
It's possible one of the throttle cables has come partially dislodged and now the two cylinders are getting very uneven throttle.
That makes the engine run quite rough. Or,
b) My guess is that one of the stick coils is not properly connected to the ignition wire. Or worst, one stick coil was damaged when they pulled them out.
From the sound of it, your bike is running really badly so it's more likely one of the main spark plugs (as opposed to the secondary).
"It is not when or how you die but how and if you truly were ever alive!" Dr. Jerri Nielsen FitzGerald