I dont have any issues with shifting. its not the clutch, but the actual shift lever right?? check your clutch fluid in your primary... the 1125's have a hydraulic clutch, and if for some reason you dont have enough fluid or you have air in your lines, it may make shifting in and out of gears a little more difficult... it could be nothing. maybe you just have to get used to it...
also, check your clutch cover on the right side of your bike... in colder temperatures (at least on my 1125R) some of the internal components, i.e. seals and what not, shrink allowing for fluid to seep out. I know this was a problem with the '08 1125Rs, but may be an issue with the '09 and later CRs too.
my R idles at about that same RPM. if you are unsure about it or want to test, do a TPS reset. to do this, turn your key to run, and make sure the engine cut-off switch is set to on, but do not start your bike. from this point rotate the throttle to wide open and hold for 1 second, return the throttle to fully closed position and hold for 1 second, repeat this 2 more times and then turn your key to the off position.