Interesting ... at least the part about the joysticks not being populated since that is the very first thing to consider. Is it worth rewiring your machine to a new harness?
My personal choice would be to do put in a new harness -- it is easy and clean (I wouldn't bother trying to jam new wires into an existing harness -- more trouble than it is worth), but limits your encoder interface options (JPac and JammASD would be the obvious choices to handle everything except the trackball. IPac not an option). Then you need an interface for the trackball (like an OptiPac or buy a trackball with the interface built-in).
I've always used JPacs in situations like this and love them, but JammASD may be more convenient (I bought a bunch of audio amp kits years ago, so that aspect of the JammASD is not really important to me). I'm not sure that there is a big disparity in price as the poster above implies, but I am always suspect of technically-minded people who are happy to spend the time on a DIY and have little experience with the products at hand.
If you don't care about keeping the cabinet JAMMA, you can just pull out the old harness and rewire from scratch. Then you would have a full range of encoder options (including IPac, as well as other options that can handle the trackball as well, like an IPac Ultimate I/O). You can use a hacked VGA cable and perhaps a video amp to connect to the arcade monitor (both available from, say, Ultimarc).
In either event, video conversion at the PC side may be required.
It may seem overwhelming, but you probably still have some research to do vis-a-vis audio and video (EDIT: meaning JAMMA amplified mono vs unamplified stereo from your soundcard and 15kHz amplified vs 31kHz unamplified video)
Good luck!
NOTE: Since you referred to Ultimarc products, I have used them in my response. There are many other options -- I just wanted to use products that you are somewhat familiar with to provide some clarity.