The tank likely is vented at the top, typically they have a chamber the fuel needs to be beneath that chamber. It would have a vent line that leads into a canister filled with charcoal, it filters the fumes and prevents the tank from forming an air lock and chocking off the fuel supply. Basically you should never top the tank the fuel should be far enough from the top to ensure you do not submerge the vent.

If a bike is not running right and particularly if it is brand new you should not keep running it.

If it running fine now with less fuel in the tank then that likely was the issue, if you feel it over heated then best thing to do is change the oil. When you do that measure what you take out and do not put more in then you take out.

You could assume that the specs on the valve clearances are correct from the factory, you would hope they are! You typically check them after the engine is worn in not before.