More good news!
I've successfully communicated with the NAOMI from the USB serial adapter on my laptop!
Just sniffing one direction during the initialization sequence and then swapping pins and sniffing the other direction, I tracked down the send and receive from NAOMI and reader during initialization in the test menu.
I decided to try unplugging the reader and see if I could fake the signals back during the initialization sequence. I wired everything including RTS from the serial adapter into the NAOMI.
One important piece of information I figured out is that the NAOMI expects the reader's RTS to be on. While off, it immediately fails the test and doesn't even send any kind of request.
Using the free version of 232Analyzer, which has some annoying limitations so that you'll buy the full version, I managed to figure out the responses to the output from the NAOMI during the test menu initialization. I didn't have the ability to program any kind of macro, so I was just copy/pasting strings of numbers for the program to send back to the NAOMI. Fortunately the NAOMI sends repeated requests several times before giving up. That gave me enough time to quickly reference the next line I needed to send back.
I allowed the game to boot and got through most of the initialization that comes up there, but it sent a different string at the end than it did during the test menu manual initialization, so I wasn't able to get the game to start.
I'm pretty optimistic that reader emulation is going to be possible with just a simple $10 USB Serial adapter. I'm currently working in Windows and may proceed with figuring out the proof of concept on this platform before porting to something more permanent like the RPi.
Just for reference, if I consider the NAOMI's output as the Question and the computer's (emulated reader) output as the Answer, I used the following to get through the manual initialization in the test menu:
Q: 2,6,64,0,0,0,3,69,
A: 6,2,6,64,160,48,50,3,231,
Q: 2,6,32,0,0,0,3,37,
A: 6,2,6,32,160,48,48,3,133,
Q: 2,7,16,0,0,0,49,3,37,
A: 6,2,6,16,160,48,51,3,182,
6,2,6,32,160,48,48,3,133,
Q: 2,6,32,0,0,0,3,37,
A: 6,2,6,64,160,48,50,3,231,
Q: 2,6,32,0,0,0,3,37,
A: 6,2,6,32,160,48,48,3,133,
Q: 2,6,64,0,0,0,3,69,
A: 6,2,6,122,160,48,50,3,221,
Q: 2,79,122,0,0,0,36,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,18,
A: 6,2,6,122,160,48,50,3,221,
I'm not sure what to make of it, but that long string that the NAOMI outputs isn't the same every time. In the test menu initialization, it doesn't seem to matter. I could give the same response every time and it indicates that the test was completed without errors.
I'll have to do some more sniffing to see if I can get through the boot initialization sequence.