Hi, I moved to an R1150R Rockster from a honda firestorm and was overwhelmed by all the new noises I was hearing. All the things you have mentioned, a search of this forum will put your mind at ease, long story short 3 years later and I have to say it's my favorite bike of all the bikes I've ever had, they are reasonably easy bikes to work on I would suggest learning to do your own work, a lot of bike shops love to run these bikes down.
Here is a list of noises and the solutions I found,
Rattle on startup on left hand side: uprated cam chain tensioner
Ticking, clicking on right hand side: butterfly shaft in RHS carb rattling. Throttle body sync helps, tried a ticker killer, also helped but some days it's louder than others, don't really worry about it.
Noisey gearchanges: learn to preload gear lever before changing gear, I find quick changes the best, don't let the transmission unwind,
there is a lot of free play in there
Rattle from heads: adjust valve clearances
Transmission rattle at tickover: Throttle body sync
Everyone has there own way of checking engine oil level but I find the only way to know how much oil is in it is to do an oil and filter change, put in 3.75 litres of oil and then use the same routine for checking the level, what I do is leave bike on side stand for 15 minutes after long spin then put on centre stand and check oil level after a few minutes, it should be around the centre of the sight glass, I find it doesn't seem to use as much oil if I keep the level on the low side as opposed to keeping it at the top of the sight glass.
As long as you can see oil in the glass it is ok to ride.
I hope your bike is ok and you get a chance to enjoy it, they definately grow on you. Cheers.
02R1100S,05R1100S(BCR), 
(2)-S1000XR 
