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Do you need pull-up resistors on PD0, PD2 and PD3? What voltage will be on the pins if the links are not fitted?
You can save components by using a 7805 regulator.
Your multiplexing needs to send 16 bits per pair of digits, 64 bits to display complete numbers, you may not get optimal speed or brightness from the LEDs.
The CD4094 outputs are only rated to sink 0.88mA so the LEDs will be very dim anyway.
Does the ATMEGA8 need an oscillator and reset signal?