Thanks for the great pics! Good to know SOMEONE can work on their pond, mine has been delayed two months due to excessive rain.
I'm certainly no expert, but it looks like you might have pretty acidic soil. Have you thought about checking the alkalinity of your water and, if necessary, liming your pond?
Also, the big brains here would likely tell you to keep a few misshapen trees and rootballs, especially if they are hardwood. They make good cover when sunk in the right places, will definitely help your small fish survive to become big ones.
Lastly, you are SMART to check in here where you get expert advice (not mine, obviously!) for free. Despite being from Maine, you obviously have learned not to take anything for granite!