Are you letting it idle with the choke on? You should normally push the choke in half way as soon as it starts, and keep nudging it in as the bike warms up.
There is no timing adjustment on these bikes. Noises and whines are normal.
Has the bike been sitting for a while with old gas in the tank? if the rear carb is gummed up a bit it could be running very lean on the rear cylinder, which would make it run hot. Its also possible the carbs are out of balance, and need to be synchronized.
If the bike runs normally I would not worry too much about how it behaves when its idling.
I would do two things: pull the spark plugs out and see if they are black (running rich or not firing correctly) or if they look burnt from running too lean.
the other thing that can only help is go get a pint of SeaFoam from the auto section at Walmart, and put 4 ounces in a full tank of gas. See if the bike seems to run any better after that.
Since you mentioned the valves sound noisy, do you know how any miles it has been since they were checked/adjusted? How many miles are on the bike now?