So I finally got this working on my naomi 1!

(what a finicky little thing it is)
I've basically read through the thread a couple of times and tried what a number of users have said as a trial and error.
Things I did:
- Installed headers so I can get into firmware mode
- Updated the firmware to 1.44 as per Shin's post
- Program my Virtua Stick High Grade stick via layout config mode (TEST+SERVICE > TEST> Select > Start > B1 > B2 > B3 > B4 > B5 > B6 > TEST)
- Since I updated to 1.44, I was able to toggle between "JVS data signal level adjustment" when pressing TEST while plugging in the power
I noticed when it works, the MP07 LED flashes quite quickly and then it'll be come solid when the Naomi logo loads up. If it's just blinking like in normal mode, then it never works, I simply unplug power and reconnect using the TEST mode and restart the Naomi.
I've currently got the MP07 plugged into a mobile phone charger, but I will look at looking for another 5v location as the normal CN12 is already being used for either my Pi or a CF card reader.
I actually don't know how to "enable or disable" the options I think I fluked it as I was able to cycle through Sega JVS and Namco JYU jvs
I haven't tested it any further on my Naomi 2 and/or with other devices as I'm still trying to digest what it was that I did to make it work and hopefully it keeps working
All those guys having issues with Naomi's, please see how you go with updating the F/W and seeing what behaviour the PCB does when turn on the naomi - remember, if it's fast blinking - it should get a steady led once the Naomi load screen shows up and it'll show up in the JVS test menu. If it's just normal blinking, unplug the power, hold test when you plug power in and reboot the naomi (this is of course if you're on 1.43+)
Edit:
- I've tried configuring the Hori Fighting Edge for PS4, but it's lagging pretty hard. It's like you have to hold it before it registers, this is directional and buttons. The mapping is also weird, even though I map coin, start, b1 to b6, I get something totally different.
Will try mapping other sticks.