Haven't had the boat long and have been using just the the flush port. Decided to get muffs and first time I used them was after the impeller change so yes had no reference for before impeller change.
Yamaha advises not to run on the flush port.(look at the size of the water tube!) Some folks do it and run OK at idle. It is not a good idea to run at more than idle on the flush port. A dry impeller can get fried rather quickly.
It was mentioned that the water pump needs to be submerged in water to pump. It's design is not self priming. The muffs generally work because they flood the pump housing priming it. If there isn't enough pressure or water volume to flood the pump, the pump won't work and the motor will be starved of cooling water