I think that what you are planning is wise based on the pond's location and your son's plans.
However, I'd fully drain it as soon as possible and start to rehabilitate it. You are going to need the intense Nebraska summer sun to make it feasible to work the muck.
I can't tell from the photos if it has a dam. I assume the drain goes through or under a dam. If it does, I'd breach the dam, and the let all the water out now. If if doesn't have a dam, I'd rent a trash pump, and pump it dry to the point where you can keep it constantly draining.
You might be without the pond for the whole summer, and maybe even next summer while the muck dries, but it would be worth it. If it has several feet of muck, it will be some time before it will be dry enough to get the crawler and tractor in there -- been there, done that -- up to the belly of the beast (65 hp beast). But, with having a JD350 that you can use a little bit at a time -- and a tractor big enough to help boost the crawler out if it gets mired in the muck, I'd go for it. After a month or so of drying, and before burying the crawler, you probably would do yourself a favor if you rented an excavator or a trackhoe to get started around the periphery. That way, you can get below the wet level of the muck from a safe distance, and it will help drain the muck in the middle. Even a small to medium size excavator can move an incredible amount of muck in a day, especially if you put 3-4 foot bucket on it. If you are renting an excavator, they will tell you that you are crazy for wanting such a big bucket, but it should be very easy digging.
Good luck,
Ken
