Have you set the sag on the rear shock yet? If there's too much preload, that will cause the seat height to be higher (and it won't handle right).
How about cutting an inch out of the seat top, especially towards the front? Also, if you narrow the top edge of the seat, it has a similar effect as well, since your legs won't be as splayed when stopped.
I've read articles on lowering the subframe, they cut a small amount out of the 2 lower arms right where they bolt to the main frame, thereby lowering the seat height. A bit of welding seems to be the only item required. Be careful that it's not dropped so low that the tire hits hard at full compression (pull the spring off the shock to check), and that the muffler still fits properly. Lastly, this mod will not affect the seat height at the front of the seat since that mounting point remains the same. In conjunction with some cut foam however, it makes the total height lower.
From a $ standpoint, having the suspension lowered should be your last step.