Thanks Fox1, that last post helped me out immensely. It's strange, looking at the board, it looks to clearly say "flip the switch up and get this, flip the switch down and get this" but in reality, the sticker on the board is only indicating what some of the dipswitches are, not necessarily what they do.
For example, Dip 2 shows JVS I/O with a line at the top of switch, then JAMMA with a line at the bottom of the switch but the manual indicates that the switch operates in JAMMA on the off position. So strange. But now the confusion I had when I thought JVS I/O and JAMMA were flipped makes total sense.
Does the manual say anything else about the composite video mode? The image on screen looks the same with dip 3 turned off or on. I haven't flipped the switch while the system was on, but I powered down and tried both ways and the image is the exact same. Is it possible the switch itself is busted?
So now the confusion with JVS and JAMMA mode in regards to sound now make sense. But I wonder why plugging the board in without the JAMMA-to-MVS converter achieved loud, full sound before it fried my speakers (and possibly the sound amp).
edit: I don't know if this changes anything, but I had the board's sound running in mono mode when I tried it without the converter and got sound. Running the board in stereo or mono right now nets the same result.