Well, it's a labor of love.
It's recommended to keep a pond (lake in your case) journal, so you can better track progress.
As the process will be ongoing, it may be beneficial to invest in some fish traps, nets, and seine nets. These tools can go a long way towards achieving your goals.
If you ever electrofish again, that is a great way to cull large amounts of fish.
You mentioned that the 'upstream' pond is frequently intentionally drained into your pond? I would try and stop that process if possible.
