Yeah, ended up figuring it out after looking at it a few minutes and remembering everything from Japan is built with bass-ackwards engineering. lol
However, after trimming 1/4" off the rod and adjusting it until the lock nut was bottomed out on the rod nut the brake pedal still sat way too high for my liking. It was roughly the same height as the top rear edge of the peg. Only way I found to get it down to an acceptable level was to remove the lock nut from the rod then screw the u-bracket/nut all the way up to the fixed nut on the rod. Of course this eliminates the mechanical lock and adjust-ability offered by the additional lock nut.
Put it all back together and left it loose...going to ponder it for a day or so and see what other option I can come up with. Might try a thinner nut, but doubt even it would allow the adjustment needed to get the height right.