When engines do not run right. Suck(fuel and air), squeeze(compression), pop(ignition), fooie(exhaust)
I guessing your problems are either in suck, or pop.
To figure out which is your check engine light on. If yes pull the code. Check your spark plugs, are they both firing, are they both in good shape. If yes, your ignition is fine.
For air first; check your filter, is it clogged; are their any vacuum lines, bypass screws that have fallen out; any other easy/obvious stuff. If your done with the easy stuff, check the vacuum balance between cylinders, and adjust your idle speed (screw by the throttle bodies rh side I think). If your vacuum is balanced and adjusting idle speed doesn't help continue to fuel.
Fuel, take your air filter off and while the bike is running and spray carb clean at each cylinder, does the bike like it when you spray at one cylender. If yes that cylinder is not getting enough fuel. Throw a can of whichever snake oil injector cleaner you want in and see if that helps. If not this could get complex.
If you can't get the bike to run better no matter what you do check squeeze and fooie.
Hook up a compression tester and see if you have compression on both cylinders.(961 ∼ 1 471 kPa (9.8 ∼ 15.0 kgf/cm2, 139
∼ 213 psi)
Is your catalytic converter plugged? Has a poorly done custom exhaust been put on? Has the exhaust been crushed?