It actually would be trivial to add the Physical/Special split for moves to Kalos Crystal, the issue is more with move distribution. Just adding it directly would result in some types with no moves of a certain category, so it would need to have more new moves added in, which would require removing some existing ones, since Kalos Crystal is already pretty close to the max number of moves. It's totally doable, but would require a lot of reworking things, and I'm far enough removed from this project that it's not really worth doing that.
I have debated doing a more polished version of Kalos Crystal in the future, but that would need to be after I'm finished with Black and White 3: Genesis, since that's where I've been putting all of my effort recently.
As for the clock, I didn't make any changes to the reset system, so it works the same as in vanilla. Which unfortunately means that it requires generating that passcode, like the vanilla games do.