Need expert opinions - Time for valve adjustment?

[SovietRobot]

Sounds like you have some sort of a vacuum leak never dug far enough into my bike to known where to go from there but those are all symptoms of a vacuum leak. Maybe behind the throttle bodys?

After I replaced the broken stock CCT with the manual one, the idle screw works now.

It still has decel/partial throttle roughness though.

 

[TownsendsFJR1300]

I'd try re-syncing the throttle bodies now being you have the other problem solved and its idling... If one (or two) cylinders is running harder than the others, it'll also cause the roughness. (When syncing my 07, I re-check the sync at 4,000 RPM and adjust accordingly-it helped clear up 80% of the buzz associated with an inline 4). No roughness, nice smooth decel and accel.

Disconnecting the battery and re-setting the ECM while the tank is up wouldn't hurt either...

Also, if the manual tensioner is still a little tight, I'd loosen it up just a very lttle bit and find the sweet spot. You don't want that chain too tight..

 

[FinalImpact]

. . . . .
Idle screw does nothing, so no matter what i set it at it sits around 13-1400RPM but bounces around. I've tried syncing the throttlebodies several times but can never get it right.
Performance is great, the problem is just idle and partial throttle(where it lugs and sounds like the exhaust valves are sticking open).

Had to look back at some history. . . This also sounds like a vacuum leak but later on you say it was cured by the manual chain tensioner. That seems odd to me like. . .

It's been a while and you have new issues now. Lets see how it all goes. . . .