What are those little holes......

[chumbucket]

I wouldn't be too concerned about when on the muffs. You can't deliver the same water volume from a garden hose that you do when the boat is in the water. That's why you shouldn't over rev your motor when on the muffs.
I had a 225 Evinrude on my Grady mounted on a bracket. I believe that the factory mounted the bracket a bit too low. Those exhaust ports were under water with the motor down and the motor didn't like to idle very long without dieing out unless I tilted the motor just enough for them to clear the water line. Then it idled fine.
On a side note, I forgot how clean my Yamaha was.