Hey Josh, welcome!
Job 1 is going to be getting your pond to hold water. Wihout that, everything else is futile.
Wherever you have sand and gravel, you will probably have to cover it with a thick layer of tamped (or "puddled") clay. You may have to dig deeper, because the clay needs to be at least a foot thick, and preferably 18". You can save your clean clay in a special pile, and use it for sealing later on. If the stumps are in sandy areas, they will have to go. Do you have access to a backhoe?
Good luck on your project. It sounds like a lot of work, but you sound determined to succeed.
