There seems to be a disconnect between what I'm saying and what you're doing. Please refer back to my original schematic if you're planning on using the nine board array. If you're not planning on that, do what you like.
If you are doing the nine board array, you have to arrange things so that all of pie-shaped boards are EXACTLY IDENTICALLY THE SAME and all of the slice-of-bread-shaped boards are EXACTLY IDENTICALLY THE SAME.
I strongly suggest and recommend that you multiplex ALL of the hour and minute LEDs. This is both to maintain symmetry in the boards and to have any chance of having the brightness levels of the LEDs about the same. With the minute LEDs multiplexed, each illuminated one is only one for ⅛ of the time. With the hour LEDs directly wired, when illuminated, they will be on 100% of the time. The brightness levels will be wildly different.
Yes, if you do what I suggest, you'll need 9 times more resistors as I have already explained. That will be a difference in cost of less than a buck. But it will work and look good.
I suggest you draw a separate schematic for each type of board, and see how the connections work.