Query approved.

Check Engine mounting screws - this may not be the case.
you mentioned fluctuation in RPM and also Engine feeling rough - may be carb needs overhauling. you are getting a whopping 58 kmpl implies you are running lean. I am using 2005 unicorn(37000k) and I am getting 51~54kmpl in city conditions and 62~64 on highways. I've tried some combinations of "Fuel screw" and I noticed that if you are running richer the engine feels smooth and the opposite with lean mix (leaving alone other things). Currently I am running with 2 1/2 turns out and I am happy with this setting, no cold start issues and also good pickup.
did you try unjamming the fuel screw? There are some sprays like zorrik, wd40, and something from wurth. or simply diesel mixed with gear oil.
clean the carb with paint thinner with a syringe to clear off all the deposits, use scothbrite pad to clean the slide...etc etc.....

because you took care of the bike in a very good manner the issue may be with the carb setting.
ride the bike at very high speeds to clear any loose carbon deposits in the engine - this is what mechanics say.
Currently I am using castrol power 1 racing and the results are good. Don't know what oil to use as the draining is due and Castrol power 1 racing is not available now and no other synthetics are available in my area.
I used Nulon engine oil treatment and I cant say I feel any real difference but only psychological. Also check your chain lubrication - I usually remove the chain and soak it in diesel and spray water and the chain becomes dirt free.

First do check with your carburettor.