Ok, I can follow that nicely!
One question - for the minutes, where the display is only 0-5 & 0-9, you could probably get by with smaller arrays.
Ah - just occurred to me - you probably have double-six as the domino acting as the display, so you need 12. Can't seem to scroll back to the original post while I reply, will have to go look at that again.
Anyway, now that you have a seperate variable for each digit, I don't think you have to worry about the >> as you don't have the shift registers tied together serially.