First off, check out the complete Naomi wiring diagram:
http://www.sega-naomi.com/resources/manuals/NaomiWD.pdf
The Naomi requires 4 different kinds of line potentials:
+12V (red wire)
+5V (yellow wire)
+3.3V (brown wire)
GND (white wire)
If these voltages sound familiar, that's because they're all standard ATX voltages (i.e. you can get these voltages from a computer power supply). As a matter of fact, there are people who sell adapters from ATX power supply to Naomi (search ebay or google). The two big blocky connectors on the Naomi motherboard (CN1 and CN2 in the wiring diagram) are from a Japanese company called JST, from their VL line (search under wire to board connectors). The datasheet can be found here:
http://www.jst-mfg.com/product/pdf/eVL1.pdf
The smaller connectors going to the I/O board (CN 6) and GD rom drive (unlabeled on wiring diagram) are also from JST, but from the NH line. Datasheet can be found here:
http://www.jst-mfg.com/product/pdf/eNH.pdf
If you want to connect those to your ATX power supply, you can do so through the 4 pin peripheral connectors (the ones that go to your harddrive and CDROM drives) as they only use 12V, 5V and GND. The Molex part numbers are:
Pin housing: AMP 1-480426-0
Pins: AMP 60620-1
As for availability of all these parts, the JST connectors are rather hard to find. On the JST website, you can search for exact part numbers and it will return a list of distributors. The Molex parts, on the other hand, are extremely common and they (or their equivalents) can be found almost anywhere.
TODO:
1.Identify the third, non-VL connector on the Sega power supply (seems to be AMP brand).
2.Find sources for JST connectors.
