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Well it was a difficult answer since I built this cube in 2012 and have forgotten most of the stuff I did but hopefully it will help you.
Correct - See table in question 6. Everything connected to the pins with an asterisk can be left off.
FTDI basic is a USB to serial board that allows you to program Arduino Mini Pros (these don't come with a USB connection making them smaller than say a Arduino NANO). Search for "FT232RL 3.3V 5.5V FTDI USB to TTL Serial Adapter Module Arduino" on eBay. They are around a couple of dollars. I replaced the male header with a female header since most of the boards you will be plugging into have 6 pin male headers. You can also use a 6 wire female to female cable. Do a search for "dupont cable" on eBay and find one that has female to female headers.
The power supply has a regulated 5V output. The output is connected to pins 1 and 12 of SV4 on the anode board. (Actually it is highly likely that I forgot about the power supply when designing the board).
Originally I was planning to run separate data lines to the RED, GREEN and BLUE channels. This would reduce the number of clock cycles to refresh the display from 192 to 64. In the end, it wasn't necessary so I only send data to BLUE IN. All the shift registers are daisy chained. So while they still exist on the anode board, they aren't used. (Probably should of removed them)
Yes, you can program the chip in a UNO and then unplug it and solder it in the board. If you use a IC socket, you can unplug it and reprogram it on the UNO otherwise you need to use a FTDI programmer (which is what the 6 pin header is for).
You can also use a UNO board and just connect the following pins
UNO =+= ATmega328 on anode board
D2 =+= Pin 4 - LATCH
D4 =+= Pin 6 - BLANK
D11 =+= Pin 17 - BLU_IN
D13 =+= Pin 19 - SCK
D5 =+= Pin 11 - 74138 A Input
D6 =+= Pin 12 - 74138 B Input
D7 =+= Pin 13 - 74138 C Input
D10 =+= Pin 16 - SWITCH_PGM (Connected to BLU_OUT on SV4)
D9* =+= Pin 15 - SWITCH_SEQ (Connected to GRN_IN on SV4)
D12* =+= Pin 18 - MSGEQ7_STROBE
D3* =+= Pin 5 - MSGEQ7_RESET
A0* =+= Pin 23 - MSGEQ7_OUT
+5V =+= Pin 7 - VCC
GND =+= Pin 8 - GND
The schematics for V4 and V5 are the same. The difference is that V4 (which was the version I built) was designed for a single sided board and hard wired connections between the DM13A outputs and the LED cathodes. (192 wires). The V5 board was auto-routed using the Eagle software's auto routing system. It requires the board to be double-sided with through hole plating - something that you need to get manufactured by professional PCB manufacturer.
The Red output on RED_76 is not connected as it is the output of the end of the chain of shift registers.
SV1 on the anode board has a eight wire ribbon cable going to SV2 on the display board. On the display board, wires run down from each of the 8 layers through a small hole and are soldered on the underside of the board to SV2 (hand wired). You could eliminate SV2 and wire these directly to the female plug that plugs into SV1 on the anode board.
It is not used so I just joined it to ground.
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