If you leave the front end alone, most don't notice the handling issues from just lowering the rear. But they are still there. It is when you start altering the front end...
I would highly recommend having the seat modified. You can even do it yourself with serrated and straight carving knives. You don't just want to cut it lower, the most important thing is narrowing it. Look at the seat front - how much it is spreading your legs when seated. This makes your legs splay outward, not straight downward.
Seat building 101:
Go down to the local hardware store and pick up a can of spray foam insulation. Remove your seat.
Pull the staples from the seat cover and foam padding.
Put the seat base back in place.
Hold a garbage bag in place over the seat base.
Spray the contents into the garbage bag, and hold/tie the bag closed - the contents will be STICKY.
Sit on the bag - forming the foam inside to your backside.
Sit on it long enough to let it set.
Now shape the seat foam as closely to the bag/foam as possible.
Recover. Get a heavier stapler and some Stainless staples - normal ones will rust quickly.
If you really want to get fancy, Kemmler makes the best foams and gells I have ever used. You will really like the Air2Gel foam. And you can buy them direct in small sizes for motorcycle seats.
SHOCKtec Gel & Air2Gel Products