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You're hearing noise from the lower unit correct?
Yamaha had a gear change in 2006 just to address this. In your case I have a couple questions and things I want you to try.
First, is this the same prop as you had last year? Do you hear the noise when the engine is in the water or just on the hose?
Yamaha also came out with a new hub design. Try this, take the prop off and turn it 1/4 turn and reinstall. Also make sure the splines are well lubed and the prop nut is tight.
Also check the gear lube that it is clean and new.
Do these and respond and we will go from there.
I have had a few conversations with Yamaha service about this. In fact I have a 2010 F150 in the shop with the same thing. As I posted Yamaha changed the gears in 2006, so that is an option, replacing the lower unit, although expensive. I've had a couple that moving the prop on the shaft helped. Usually having the lower unit under load in the water and higher rpm and the noise goes away.
I bet you have a stainless steel prop. What is happening is the weight of the propeller and the lack of a load along with slow rpm and the shifter and gears are "rattling", "knocking".
Now if you get a ratcheting sound when trying to put it into gear, that is another problem.
So your options are to replace the prop, replace the lower unit, or don't run in gear out of the water.
Not a real common problem but one I've seen a few times.
Yamaha says no damage. I've pulled gearcases apart to find no wear at all!
As long as there isn't noise while running you should be fine.
Try it with the prop off and if no noise, that is the problem.
Try what I posted above, it may help.
No that is normal.