Your pond is breathtakingly beautiful. I could live there year round ;)
The culvert, as well as any extreme weather event such as flooding, could be the portal for lack of a better word. I did see more than just a culvert in that photo so thanks for explaining to me that you're the starting point of a huge network of lakes. Makes sense given you indicated you were spring fed I believe.
If you share decent photos of the crayfish you have, I can most probably identify it for you. Please know your overall description leads me to believe you do have the Rusty Crayfish. There used to be a Canadian Organization where one could learn more called "Protect Our Waters". Perhaps there is material available from them at your library?
The overall description of your turtles sounds an awful lot like Chelydra serpentina. Cut and paste that scientific name into a search engine for images and see if it's a match. Bet it is.
In terms of the pond "management", I don't know enough about it to "mess around" with it. I leave it as is, as nature intended it to be.
Nature did not intend for non-native crayfish to be in that body of water. That's an accidental introduction as a result of sportsmen tossing out left over bait. Think of our waters as you would the blood in our own bodies. Blood acts as a transport medium carrying various substances from one part of our body to another while additionally protecting our bodies against organisms. Pollute your blood by introducing foreign substances, and it's ability to function as nature intended is impaired. Same deal with our waters.
I don't know of any other interactive forums where you could learn more about ponds however if you find one, please share the link. I only post here for all practical purposes and the vast majority of forums I visited before I joined here didn't have members who could or were even interested in differentiating between a native and a non-native species. Many thought the term invasive was a joke. The only forum that I stumbled upon where members seemed to actually care about the environment other than here was the North American Native Fish Association. Which is a quality organization by the way. Many of the people at that forum would be able to help you differentiate between which species belong as intended by nature and which species don't belong which could help you feel more comfortable managing your pond. That NANFA organization is extremely progressive and environmentally conscious. They have a line up of hands on professionals who address these types of issues daily.