CARB-SYNC!!!
Had a similar problem on my GT650 sportbike. Started running rough for apparently no reason. Like you, I replaced the plugs. I sprayed carb cleaner into the carbs, yet still running rough.
Built a carb sync tool (very easy) and in less than a minute my problem was solved. My front carb was drawing a bit more vacuum than the rear. A coupe of turns of a single screw and she was purring like a kitten.
Building sync tool:
Items needed:
Wooden yardstick
8' of clear tubing (used aquarium pump tubing)
zip ties
some tube fittings (1/8" to 1/4")
You basically make a U shape with the tubing (leaving about a 2" loop at the bottom to prevent kinking) and zip tie it to the yard stick. Keep the lines separate and parallel.
You should have a foot or so of tubing free at the top (needs to be long enough to reach the vacuum lines on both carbs (adjust if needed).
Fill the tubing with motor oil (I used some Royal Purple I had laying around as it would be more visible). You want to fill it with enough liquid so that when it settles it is just about halfway up the yardstick. MUST NOT HAVE AIR BUBBLES!! If you do get some, squeeze them out.
I am not familiar with the 1100 at all, so you would have to locate the proper vacuum lines and adjustment screw.
Fit the appropriate tube fitting on each end of the tool. attach one end of the tool to the forward carb vacuum line and the same for the rear.
Locate the adjustment screw. Start the bike. You will see the carb with the stronger vacuum pull the liquid up it's tube. If the vacuum is too strong you will have to shut off the engine and adjust the screw. Repeat until the liquid stays as close to even in the tubes.
Whew!! It really is easier than it sounds.
Tool should look something like this to give you and idea(not mine):