Mate, this happens normally in virtually every bike gearbox. That is why the top corners of dogs eventually get rounded off. In an effort to make the gears in these bikes take load/torque, Triumph spin the box at near engine speed. The upshot of that is that there is less time for the dogs to engage as they whiz past their slots. Undercutting the gears will improve positive engagement but will also slightly enlarge the length of the dog windows allowing them to engage easier. If one is going to undercut the gears on a rocket, I would strongly suggest NOT using the angles one would use on a drag race engine/bike. Shim the box properly as well to remove slack so the gears cannot "get a run up" and smack into the next object( maybe a circlip) with as much impact. Having said all that I have done very few boxes here. I think whilst the spiralox clip seems like a good idea, it would be worse. I would rather have one thick rigid clip as it would seem to me that the two thin winds of clip will flex more in service. Machining the groove deeper will disturb the surface hardening of the shaft promoting a crack. Maybe look at various clips and see if a stiffer one can be found and install it correctly. If a lunatic like Ruzz can ride about with carefree abandon (gaily) with 240+ ft lbs of torque on the stock circlips and a friggin 8" car tyre they should be ok.