Gentlemen
I had replaced the rear fender last January for the very same reason, the previous owner thought it would look cool to chop the thing just below the license plate mount. That owner was a seasonal rider, and I ride all year round and need the protection that an intact fender affords. The replacement fender cost just over $100 purchased online at
Boats.net.
No, the air box did not need to be removed, however the cover over the intake snorkel beneath the left side cover does need removing in order to get to all the fasteners, and components attached to it. The rear wheel needs to be removed also, as with the top tray and metal cross pieces, and various electronic black boxes. You will also be removing the tail body work - including the tail light module. When I did it, the tail sub frame was stripped bare - although it did not require removal.
It's not a pain in the @ss, but it
is rather involved. My suggestion would be to take your cell phone or digital camera and document the whole process of digging it out, that way you can refer back to the pictures for proper reassembly - especially if you are forced to take a week or two break before completing the job.
All you need is a few wrenches, a screw driver, and some patience; the FSM is not essential, however it is a good resource if you have one. Bare in mind that the part number is different from the 2nd Gen.'06-'07 and the 2nd Gen.'08-'12 bikes. The differences are not apparent until you get deep within the bowels of the bike. Be sure you have the proper one before disassembly.
Pictured below is my '06 bike with the fender stripped out. I was going to use it for the '08 that I had just purchased, but found out it was a different piece of plastic. As you can see, the air box is undisturbed.
Don't be intimidated, by the nakedness, it will go back together just fine.
All that said, the job can be done successfully in a day, just be patient, observant, take lots of pictures, and enjoy it; after all these things are supposed to be fun!
Brodie