If you chop the springs too much and don't make up the difference with a spacer, it can unload at full extension and you will get a lot of rattle.
I chop the spring to get a stiffer suspension and then make up the difference with a spacer. It all ends up a little taller than stock, so it's probably not what you want.
Like Texas said, it would be better to raise the forks in the clamps by about 1/2" to 1". That will lower the front end by that much. The problem, as you mentioned, is that the air holes won't line up anymore. Will the air holes at least get blocked? I find it's better to use a slightly stiffer spring (I do it by cutting), then use no air. Then there's no stress about getting the pressure equal etc.
