Temp guage runs half way

is your thermistat working ok ?

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.

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.