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shift registers are fine in you run them fast enough. If there is still a flicker you just add a transistor to turn off the LEDs while you are shifting.Oh, yeah - for persistence of vision you probably wouldn't want the shift registers.
You could use a LDO regulator and pre-regulate it's input voltage down to 7 Volts or so. Then you may not even need a heatsink.
You almost have enough IO pins to do away with the latches all together. If you used a PIC with more IO, you could save some weight that way.
One question however. How are you going to set the date and time on your clock?