Low idle when clutch is in?

My bike seems to idle well when sitting (around 1200 rpms or so) but when I am riding it and engage the clutch to switch gears up or down the idle drops way down and it wants to almost stall out and it would unless I rev the engine up a bit before I shift. It never used to have this problem. When doing a visual inspection I noticed that one of the spark plug cables is kind of just sitting on top of the plug, doesn't seem to be locked on like the other one. Would this cause that type of problem? Also the engine seems to be making a fair bit of knocking or popping type sounds are whatever they are called which isn't normal for this bike either. Last year it was running like a top. I'm not too mechanically inclined so I don't work on the bike myself. I have a guy who had been working on it for awhile. He replaced the rear or the front cam chain tensioner as it was somehow broken off and part of it was in the bottom of my oil pan when I had that replaced. Any suggestions on what would cause this idling issue? Would it be as simple as just needing to set the idle a bit higher? Anything to steer us in the right direction would be appreciated.

If one of the plug caps is just sitting on the plug then you need to either make sure it is seated firmly or replace it with a new one. This is very easy to do. With a cap just sitting on the plug there is a god chance that cylinder is not firing and this can sound like a rattle or knock. Fix that and it may fix your "clutch issue" and if not then at least it's a step in the right direction.

Yeah make sure the plug boot is locked in first. The symptoms of only idling bad while in gear can be a separate deal, though I doubt it.

If the plug doesn't fix it than have your mechanic guy adjust the clutch, what can happen is the clutch cable stretches or the clutch cable could have came out of adjustment after resembling the engine during the cam-chain tensioner job. Causing the clutch to not disengage all the way.