I recently purchased a new 2000 400ex. I absolutly love the bike.I ride the desert exculsevly and as such changed out the rear 20's and bolted on some ITP 22",s... Major loss in both low end and top end. What would be the proper front and rear sprocket set up ? Bike is stone stock...

 

If you run a c/s sprocket one tooth smaller you'll pretty much regain the original gearing for about $15 or of course you could run a rear sprocket about two teeth bigger for considerably more money.
Sidewinder sprockets web page will give you the precise ratios for either option.
The taller tires are responsible for the loss of bottom end and a corresponding increase in top end, so I'm a tad confused as to why you don't get an increase here