I know the fuse box is behind the left hand grey plastic tank cover on the ABS bike, but what's behind the right hand one? There's a bit of space on the non-ABS Tenere here (I've got accessory relays and fuses behind mine). Other than that removing the snorkel will buy a bit more space under the seat, or fit a tool tube somewhere for your tool kit and use the original tool kit location?
Oh, and welcome to XT660.com too!