The best advice I can give is to work with what the land is rather than trying to impose on the land a vision of what you want it to be. You’ve got places that want to be ponds, which are a valuable feature for a permaculture design, work with them, rather than thinking in terms of leveling them.
Woodland is valuable in its own right, you might want to think about what parts of your site should be encouraged to regrow as woodland. Windbreaks, habitat, water retention And water transpiration. Integrate some human productive species in there, like chestnut, persimmon, mulberry, walnut and the woodland helps feed you as well ;)
Think about how much land you actually need to be “cleared” and for what purposes?
What are your goals and how do you want to pursue them?