This cabinet was originally something other than JAMMA or Neo-Geo (I don't recognize that smaller harness, but it's likely an older, pre-JAMMA vendor specific standard). The adapter board that's there makes it the slightly modified JAMMA that's used by Neo-Geo 4 slot motherboards. It also appears to be numbered backwards!
The cabinet probably lacked a test button, so it was added in, hence the stray wire, and they needed a ground for it, hence the stray ground wire.
The red wire probably goes to the Neo-Geo game select button as that's the position it's in.
The big yellow wire is in the position for a speaker, which would probably run up to an area near the marquee.
The JPAC should generally be compatible with the alternate Neo-Geo wiring as it doesn't move much around (mostly audio, which the JPAC doesn't do anyway, and coin/test, which the JPAC doesn't do either). However, again, your harness appears to be numbered backwards, so confirm that before you plug anything in and then account for it when making connections.