Temp guage runs half way

First question is what constitutes "overheating".
Since the car has been parked for years, the thermostat could be sticking closed.
The cooling system could have air pockets and need to be bled.
The water pump may be corroded inside and not pumping enough volume.
If the gauge goes above half way, the fans should start up. But half way should be more or less normal, not hot yet.
I would look at flow problems first, beginning with removing the thermostat and driving it without one for a few days. Also check and see if there is a process to bleed the cooling system of air.

That sounds ok, it would be more of a problem if it went over half sometimes. The only other things that may make it flucuate could be a sticky thermostat or an air lock somewhere in the hoses, but these generally cause overheating. At half way it is not overheating.

Does it remain between 3 and 4 all the time not higher? If yes, then you can say it is normal as long it remain about half way distance between "c" and "h" indicators. Good enough?

it should sit around half, may get to 3\4 on a hot day riding hard, but should not get to light on stage.
Check the fan comes on when it gets hot
Check cap or renew
Check thermostat or renew
Change coolant\flush radiator
Check for leaks
pressure test coolant system

it may even be a problem with the sender for the temp gauge, if it doesnt seem hot and the fan doesnt start

What is the problem? half way means that it is in the normal operating range.

I would be looking again at the cam chain tensioner. I have replaced 2 on my 05 so far and it was doing the same thing. the other known problem for noise in the engine like that is the valve guides are know to wear prematurely on 05's and the 03 and 04. Yamaha knows about the problem and will fix it under a one time warranty even if you do not have the extended warranty on the bike. Make sure you talk to the dealer about premature valve guide wear.