So after playing many more ranked matches, I've learned that my rules regarding the secondary timer were off. The secondary timer CAN initialize as the difference between the two timers when the difference is small...when it's large however, it only uses about 66% of the difference. The percentage scales from 66%-100% as the difference shrinks. It's REALLY confusing, and the confusion is compounded by the fact that the timer does NOT measure seconds like the Match Timer does...it moves slightly faster.
GOD DAMN IT NINTENDO