Not lowering the front will increase the rake angle slightly, which will have a small effect on the handling. Basically you'll loose a little turn-in quickness in the corners, but you'll pick up a little high speed stability. Not a big deal unless you're super aggressive in the corners and think you're Nick Hayden. I'd venture to say most people probably wouldn't even notice the difference.
As for the side-stand, I used an angle finder gauge to find the lean angle of the bike on the stand (10 degrees measured across the gas cap with stock links). Once I get my links installed - hopefully this weekend - my plan is to just grind the stop for the side stand back until the lean angle is 10 degrees again. I've read several say it isn't really necessary to modify the stand if you don't lower the front, but I'm doing it for a little extra piece of mind that it won't easily get knocked over.
If you want to lower the front to keep the stock geometry, you could use the angle finder gauge on the gas cap in the same manner to measure the before and after front to rear slope angle. Just make sure the bike is upright with both wheels on the ground when you take the measurements. Most seem to report that raising the forks 1/2" in the tree's does the trick.
