Got a 2004 here.... and I had trouble getting my battery out
.. first off, its like they airgunned the damn terminal bolts on... the battery manufacturer designed the battery on mine pretty shitty... There's no room to get a socket around the screw/bolt .... so I had fun with a screwdriver for a while putting my 150 lbs weight down and twisting.. HOpe this isn't your exact problem.
If all the stuff is disconnected, there's a rubber strip that LOOKS like a handle. The manual (both owners and service) make no mention of how to take care of this... So after finally realizing its NOT a handle and infact just a strap, I learned you have to disconnect it closest to the tank (under the bar thing).
Once all that is done, you just gotta make sure you got clean hands (no greasey paws) and just lift and tilt the battery out.
HOpefully its the same on your 01.. Hope this helps somewhat... Good luck
I went to take mine out about a month ago for storage and ran into the same problem!!! Oh, by the way I have an 01' R6....Here is What I did (as much as I can remember anyways)
1) I started with the seats(of course)
2) Push in all those round black clips with a small screw driver on the underside of the tail and remove them. There's about eight of them.
3) Remove the tail section.(Four screws, two in front, and two in back)
4) Unscrew four screws towards the back section of black tray, where the rear seat is.
5) Take out the screw next to the lock that releases the rear seat.
6) Take out the screw next to the battery(its a pain, a real tight fit).
I hope this helps, and I hope I didn't miss anything. Anyways this should give you enough room to slide the battery out. A funny thing is after I did all of this to store the bike, last week it was in the 50's here so I had to put it back in to go for a quick ride.