[RC-Monster Mike]

Yikes. Cutting one side off the battery tray will weaken the front of the tray considerably(make it prone to breaking during a nose-plant for instance). You may consider velcro or foam on the bottom to help prevent the pack from sliding forward in such an instance.
Also, in n answer to your other question(which I missed the first time), I use .5" step to clear the mud guards on my battery trays. This clears most any mud guard, but may require trimming of the screw bosses on some mud guards(compromise to allow lowest possible battery position). :)