I have been through this, it is still a work in progress. On my stock 06 with factory low seat, I was on the very tips of my tiptoes at a stop. Manageable but i did tip over a couple of times. After tearing my Achilles tendon in a crash i could no longer manage it. First round was shorter (but stiffer) springs in front and a spacer in the rear shock with a shorter stiffer spring. the bike sat about 1 1/2 inches lower but i did not get the full benefit because the stiffer springs don't sag as much. I have handlebar risers and pulled the forks up through the triple clamps, i think they are now about 12 mm higher than stock. with the rear end lowered as well, there is no negative impact on handling. In fact the bike handles much better on the road now IMHO from being lower, less suspension travel. But the suspension performance is not optimal. I bought forks and shock from an 09 Ss which, based on the published specs, will (I think) put the bike a bit lower than the XT. I have yet to install these. In stock format they may still be a little tall for me. I actually plan to get a good aftermarket shock (probably will have to be custom) to keep the remote pre-load and install better cartridges and springs in the forks. I have a former Ohlins tech guy working on this with access to Ohlins parts. If you are interested i can let you know the setup when i get it done which probably won't be until the fall. for a custom shock you could also try David Behrend at Fast Bike Industries. I have not dealt with him but he was featured in the Motorcyclist article on the Drummer website, he built a custom rear Ohlins shock.
