My CD changer (in the boot) is mounted flush to the floor, meaning I can't lift up the carpet to get to the took kit. Is this right? Only noticed it today :(

MIne is upright on the rightside of the boot. The mounting bracket attaches to three existing holes beneath the cubby.

Mine is mounted upright on the right hand side as well - that's the standard position. Mind you I still had to take a sharp Stanley knife and cut around it to enable the carpet to be lifted up and gain access to the tool kit.

mine also to the right with the mini fitting bracket

MINI modified the mounting instructions to include drilling of new holes in the bracket a few mm lower inorder to raise it off the carpet

Should be mounted on the right hand side (as you look into the boot), on the side, in front of the cover plate on that side. NOT on the boot floor!