Here's how to get rid of the moving parts related to the 1000 galon tank:
Install a fat pipe through the side of the tank near the top. On the inside bend it down smoothly (or use a nice pipe elbow) and run it down to within its diameter of the bottome of the tank. (Brace it to the side of the tank near the bottom because there will be some forces on it.) On the outside run it down the hill to the Pelton wheel.
This creates an intermittent siphon:
- The tank fills up to the level of the through-side run.
- The water starts flowing through the pipe - pushing the air ahead of it and filling the whole run with a slug of water.
- The water flows rapidly down the pipe driving the wheel until the level gets down to the opening near the bottom. ("The flush cycle.")
- Air enters the pipe, "breaking the siphon" and letting the last of the water in the pipe run out through the wheel.
This repeats as long as water is being added slower than it runs out during the "flush" cycle. (If it's being added faster, the flush runs continuously and any excess oveflows the tank.)
A small line from the bottom of the tank, through a valve, to a T in the line to the turbine will let you drain the tank if necessary. The syphon will tend to suck out sediment, at least to below the siphon inlet.
Floating crud won't be automatically cleaned out. But a gate valve in the main line will let you block the "flush" and force the tank to overflow, flushing out the floaters. You can automate that by using a 90-degree lever-arm gate valve and hanging a bucket from it under the overflow. Turn it off when you leave and the next heavy rain will fill the bucket and open the valve AFTER the floaters are washed out - then a small hole in the bucket will let it drain to prevent rust. (Position the valve so closed is 10:30, open is 7:30 and it will open fully when the bucket gets full enough to yank it.)
I assume you're tapping the 1000 galon tank to fill the 250 in order to avoid sediment and the like. You can do that by drilling a small hole in the side of the flush pipe near the bottom and tapping the 1000 galon tank to feed the 250 at a point below that small hole and above the open bottom of the pipe.
The small hole will admit air when the level gets down to it, stopping the flush and keeping floating stuff out of your feed to the 250 gal tank. Now the level will cycle between the hole and the top of the outlet pipe, but most of the rapid flow of the flush cycle will still come from the bottom, sucking the sediment off the bottom and keeping it below the level of the fresh water outlet.
Run the connection between the tanks first through a cut-off valve, then an anti-siphon valve at an elevation a bit above the small hole (though in this case outside both tanks), then through a check valve, and finally to a T in the line at the bottom of the 250 galon tank. The antisiphon valve will keep the 250 galon tank from drawing water in the 1000 galon tank down low enough to let floaters into the 250. The check valve will keep the 250 from backfeeding the 1000 as/after it flushes.
Initially fill the 1000 galon tank to above the little hole before you first open the cut-off valve and you'll never have flotsam OR jetasm in the 250 galon tank (unless you go without rain for so long that the water evaporates down to the level of the line to the 250 galon tank).
I figured out a sanitization procedure - but it takes a couple thousand gallons of clean water and a galon of bleach to do it, and again after the system gets contaminated again. Instead I'd put a suitable filter between the two tanks so I'd only need to sanitize the drinking water side of the system once (with a quart of bleach and about 500 galons of water) and it would STAY sanitized. A hose bib right next to the filter can provide a connection for feeding in sanitizing and rinsing solutions.
Don't forget to put a couple elbows in the vent tube to bend it over so rain and dirt doesn't fall into the 250 gallon tank, and a reducer (down to 1/4 inch or less) and/or a screen in the opening to keep the wildlife out.