-and my 2 centavos is worth less than usual on this subject since I STILL haven't found time to mod mine yet (on this bike):
1. If you KNOW you're going to get aftermarket pipes...keep your OEM set unmodified. You may sell the bike someday, and the pipes can be sold separately. Non-modified used bikes are usually more desirable than "modified" ones, since mods are subjective things, and not all of us are as anal about fit and finish as the other.
In short: You will nearly ALWAYS get more selling a bike if you sell the aftermarket bits separately. This is especially true with seats, pipes, airboxes, and wheels, since they're expensive mods, and styles vary widely with the individual ride.
2. You may not like your new pipes. My V-mods (another bike) were the BOMB...for about 1000 miles. Then I got tired of having ringing ears all the time, FORTUNATELY I kept my OEM pipes for warranty work and I can switch em out in 15 minutes when I wanna change. Also, some pipes will actually cost you a few HP in performance, depending on where you snap the chalk line in the curve. I haven't seen a lot of write-ups in Vulcandom about this, but when you only have 50 to begin with...loosing ONE hurts.
3. Used OEM pipes in good shape usually fetch about 100+ bones on ebay. This is because eeeevery now and then somebody dumps their bike, and since GOD has a funny sense of humor on the subject, a lot of times the bike goes down on the starboard (right)side. "modified" pipes are sometimes harder to sell. Ever price OEM pipes at the dealer? Ever see what happens to MC insurance rates when you have a claim? Just sayin...
All this is just FWIW...and I would never discourage somebody from enjoying the bliss of modifying their own scoot - BUT just wanted to put some points out there to consider.