Unfortunately, as you probably already know from buying clothes........you're almost certainly going to need to go custom, and you're certainly going to need more than $1000 as well. A bike in the size range you mentioned will be much too small and just exacerbate your knee problems unless its got an incredibly long seatpost, stem and crank.
The two best known names I've heard of making bikes for tall fellows are Serotta and Zinn Cycles, indeed I just read a little article by Lennard Zinn in the back of Velo News a couple months ago, he had built a bike for Bill Cartwright, the former Chicago Bulls coach (he's 7-1, 275 or so). I'd guess your height translates to more like a 68-71cm frame size, and I've just never seen that before
Best of luck, though!
Tom