I'm on my 3rd boat at this point. My strong opinion is that one of the most important things to do is take the time to fully document ALL the wiring on the boat. While the manufacturer's manual is decent, it is only the starting point. In this case, your boat is approaching 25 years old, and presumably has had several owners, not to mention various installers/boatyards working on it over the years.
My approach is to take the documentation in stages. Start with the batteries and everything connected to them. Identify every wire. I use Microsoft products to build a diagram. I use powerpoint, but all the shapes work in excel and word too. Once you have the battery wiring diagrammed, work outwards from there - sounds like you may have a single fuse panel. This involves trial and error, but remove each fuse and figure out what does not work. For this diagram it is important to note the fuse size, so you can ensure you have extras for each on board.
The third step is to diagram any NMEA wiring which may be installed.
Fourth is AC, if any exists on the boat.
Once all this is done, you'll know the boat inside and out, and be able to quickly troubleshoot any other issues in the future. I laminated my diagrams and keep a copy in the important documents on board.
This process is admittedly tedious, and you'll do more than your share of head scratching, but the end result is worth the pain.