I've given some more thoughts about this... There is no way to lift the gear as to where the gear sits. It's impossible. I am sure you can life the crown gear a bit using shims, but not the main gear. Since, the bottom collar and the main gear fits based on the placement of the main shaft pin holes, there is no way you can adjust this.
If I really wanted to do this, I suppose I can adjust the frames holes to allow the lower bearing block to sit up a bit higher, but that would cause other problems, and not everything will fit correctly after that.
My new gears should arrive by Wednesday. If I can't get it to sit properly at a proper height, I may use a flat surface to grind the gears to make sure that there are no high points this time, and also thin it out a bit so that it wouldn't touch the bottom carbon frame.
I received a second opinion today regarding my gears. Dr. Ben and Tom Dale took a look at it. They did confirm that the gear was warped. However, they weren't sure if the warped gears w/ high point caused the breakage of the tooth. The culprit may be with the transmission (tail) gear not being long enough. The transmission gear wasn't setup in correct length to cover the whole length of the crown gears. Therefore, the meshing was too loose.
I'll also be correcting this once the new gears arrive.