It came with a working arcade monitor: Wells-Gardner model #: 25k7401 and Jamma board...
...I can buy the arcade VGA card from Ultrimarc and connect the monitor to the jamma board, connect the jamma board to the jpac and connect the jpac to the arcade VGA -...
...I can use my PC's existing video card (I think it's a semi recent GeForce card) and download softkhz 15 and groovymame and "CRT emulator drivers". This method I would connect the arcade CRT to the jamma, connect the jamma to the jpac, connect the jpac to ?...
So, you need to find a way to get 15kHz modes out of the PC. If you're using Linux, you can do what you want, just set up the modelines with whatever card you have. If you need more explanation than that, you don't want to be using Linux
Under windows, you will not be able to use a newer GeForce card easily, if at all. At a guess, newer means anything from the GTX 400 series up, though I'm not sure where the limit lies. For anything older than that, but newer than the ancient 6000GT cards, you need a dongle. This is a device that plugs into the GPU, and you plug the monitor into that (or the Jpac, here). It delivers an EDID that makes windows think there is a 15kHz monitor connected. Sailorsat was selling them a few years back. This gets around the limit built into the Nvidia drivers, which do not allow modes lower than 31kHz without the monitor specifically saying it's ok. You can install Soft15kHz, the modes will show up, and you can select them, but the GPU won't deliver them, and will instead go for 31kHz/480p. For newer NVidia cards the dongle doesn't work either.
The exception to this are the NVidia Quadro series cards. They have a way of faking an EDID. It's not perfect, but it can be used AFAIK.
The Ultimarc ArcadeVGA cards were a revolution, but even better now is to use a regular Radeon card along with crt_emudriver. It's also much easier, and in addition allows you to get all the cool automatic features out of GroovyMAME. Calamity is in the process of updating the driver to work with up-to-date cards, but right now an HD 5000 or 6000 series Radeon card is great. You can pick them up second-hand pretty easily on Ebay or Gumtree/CL/Kijiji. The higher the card the more power it draws and the more heat it generates, so the cab may need fans if the card has two itself, as a guide. And MAME is entirely CPU dependent; the GPU is merely needed to push a video mode. Other emulators and games can be quite different, of course.
If you do go the crt_emudriver route, follow the guides for the 5000 (and up) cards here -
http://geedorah.com/eiusdemmodi/forum/viewforum.php?id=2 and after that look at the GroovyMAME setup guide there. It's slightly older, and the stretching options aren't quite right as described. Possibly just leave them as they are in the newer builds of GM, or ask in the GM forum. It's in the list at the top of the forums.
After that, you connect the PC to the JPAC with a VGA cable and a USB cable, and connect the JPAC edge-connector to the cabinet's Jamma harness the same way an arcade board would have plugged in. If everything is already wired and working, you're good to go. The JPAC has extra slots so you don't need a kick harness. There may be a few minor screen adjustments needed, for brightness and position and such. And there's a jumper on the JPAC that enables monitor protection. Putting it in the 15kHz position means the JPAC will only pass 15kHz modes. You may also want to look into monitor ranges, and there's some starting info in the stickies on the GM forum.
I will admit to never having used a JPAC, but I think that's how it all works. You can always ask Andy from Ultimarc any questions you have, by reputation he's really helpful. And I have no idea about sound, which is why I've said nothing about it
A jamma board had its own amplifier built in, but I'm not sure how you get sound into the JPAC.