You can't display video from a Jamma game on a VGA monitor. Arcade games are 15.75khz, standard VGA is 31.5khz. That said, some devices with "VGA" ports, such as studio monitor/televisions might be able to sync to it. Similarly, Apple monitors intended for Macintosh computers cannot work with that signal either. But, the AppleColor RGB monitor, intended for the IIgs, will work perfectly - it's a 15.75khz monitor. It's what I use on my test rig.
Ignore the Monitor ID lines - that's a function for newer SuperVGA monitors to be able to send an ID string to the computer to tell it the capabilities of the monitor (that's how Windoze knows you've connected a ViewSonic GS771 or whatever).
Most PC monitors really want separate syncs - but some accept composite sync on the Hsync pin - but again, you can't use arcade video on a PC monitor.
While you can't use a regular VGA monitor, you can use a monitor intended for the Commodore Amiga, Atari ST (color only), Apple IIgs, or one of the many third party monitors, like the Ampex 600, the original NEC Multisync or Multisync 2a, and many others. Sony studio monitors also frequently take RGB video, as do most other commercial video monitors.
Another option would just be to use a real arcade monitor - just remember to use an isolation transformer if you do.
-Ian