Chris--
Catching roof water is great, especially where there are drainage issues anyway (I divert water from the barn roof and driveway into the pond so it doesn't sheet across the yard, making mowing a little simpler). But don't forget that an acre-foot of water is about 386,000 gallons, so if you're down six feet on a one-acre pond that's on the order of 2,000,000 gallons. I came across one website that says a 1200-SF roof will shed about 700 gallons per inch of rain. I don't know how big your house is, of course, but I'm guessing catching the roof runoff will be the proverbial drop in the bucket, pond-wise.
I too wonder whether you have a leak. We had 1" of rain from 1 June until 15 September, and our pond lost about 16". (Of course, our soil is such dense clay that the county is actually named after it!/w3tcompact/icons/smile.gif) Sounds like you experienced about five times that amount in less than twice the time, and that doesn't quite compute. If the pond is man made, you can closely inspect the area below the dam for water; if not, just look downhill. Bentonite works wonders for leaks which are identified, but typically is applied to a known or suspected permeable area; it sinks into the bank and then expands to line the area. I also would question the wisdom of pulling millions of gallons out of a well that serves your home, unless you're pretty darn sure of the caliber of the aquifer. Sorry to say, it sounds IMHO like a bit of a complex problem. Good luck, and keep us posted!!