Well, I'll try to give you a hand. Brady pointed me at you, since I just posted a note about my cable-drive PR96 in the "shobbotter message board." Mine has been sitting idle for a bit too long, but I'm trying to get it back to work.
Do you have 3 X axis cables, or just two? The early system had 2 drive cables and a parallelization cable (fatter, with no covering) - and the only upgrade I've actually done was to apply the "two longer drive cables are the parallelization cable, too" modification. It removes some friction.
What speeds are you moving? One place you can get into losing steps on the oldsters is by running the axis faster than the steppers will go - especially if you are reading things from the modern drive era. As far as I recall I might cut at 1 inch per second and jog at 2.
Look for bumps and feel for binding of the stalling axes. With the power off, roll the axes by hand. A dent in the uni-strut can make the wheels bind.
Another issue with the encoders is running the encoder wires too close to the stepper wires - you can get interference.
The control software can (IIRC, and it's late so I'm not checking the manual right now - if the manual is even the same version as the software) be set to ignore or pay attention to the encoders. At some point the official word was to ignore them, as the newer tools moved away from using them. IIRC, I still look at them, as mine have not been problematic.
I also had some early movement issues from using a long unshielded serial cable between the controller and the computer.
I have no idea about the diagnostic output, though I can eventually check what mine says.
Take some pictures, I'll try to do the same. Off to bed for now.
PR96 from May 1997 - one owner, too little use.
Cats, Coffee, Chocolate...Vices to Live By.