Hi desh_thiere,
1) I've always used JPACs on fixed frequency 15 kHz CRTs, so I'm not sure I can answer that. I guess the best you can do is ask Ultimarc, then come back and tell us.
2) If you're not using MAME, then setting vmmaker.ini is enough. If you're using this for Model 2/3, then just a few video modes are going to be required. Place them in ReslList.txt, then create the modes, and use Arcade_OSD to get perfect centering of them (be aware you need to have at leat 17 active modelines in order to be able to edit modelines dynamically in Arcade_OSD).
3) You can simply use a 24 kHz range in vmmaker.ini, like this:
MonitorType = "CUSTOM"
monitor_specs0 23900.00-24900.00, 55-65, 2.91, 3.00, 4.44, 0.451, 0.164, 1.048, 0, 0, 480, 768
However, this will apply once Windows is loaded, there's no way to have the computer boot at 24 kHz.