The box to the left connected to the Jamma harness is the Capcom I/O board.
Info here:
http://www.solvalou.com/arcade_naomicapcom.php
There is more than one type of I/O board, the Capcom one and the Sega ones. Research this.
The NAOMI 1 motherboard is the tan box with all of the wires connected to it.
NAOMI 1 is tan, and so are the carts.
http://www.system16.com/hardware.php?id=721
NAOMI 2 is black and so are the carts.
http://www.system16.com/hardware.php?id=725
You can play NAOMI 1 games on a NAOMI 2 system, but not the other way around.
The power supply is on the bottom right and is an original SUN power supply that was used with NAOMI 1 boards. It supplies all of the correct voltages needed for the NAOMI.
You can use a computer power supply, research that before going that route.
The black box with the chrome piece is the NetDimm board, which allows you to Netboot, or load games via a computer, laptop, or RaspPi.
There is also one that looks similar just called a Dimm board (pictured below) which lets you load games via a GD-ROM drive (not pictured), but the GD-ROM drive is not needed if you are Netbooting with a Netdimm.
Both the NetDimm and Dimm boards are basically memory boards, 256MB, 512MB, or 1024MB.
DIMM Board:
NetDimm board:
You should upgrade the firmware to the lastest version on the Netdimm and you will need a security PIC CHIP for it as well.
You should upgrade the bios on the NAOMI board as well.
Once you have everything up and running you can load games from a computer or use a RaspPi with an LCD and even load games Via cell phone WIFI.
All of this is my understanding of NAOMI, but I'm almost as big a NOOB as you are with it.