Ive got the '98' TDM and as far as i know its the same bike essentially.
The battery is just one job that seems over complicated.
Seat only, needs to come off, you need to remove the pump from the frame cross member under the seat [directly above the battery] and wriggle the battery around to get it out through the gap. The only other option i could think off was to drop the whole rear end out, but the way i discribed is alot easier..........