Without being able to see exactly what you have or trace wires, etc. I can't offer much help troubleshooting.
A simple system may consist one or more batteries wired together in parallel and charged simultaneously by the alternator. The system is controlled by a single 'on-off' master battery switch, which will kill the power to the entire vehicle. Ford issued a
bulletin on March 1, 1999 which prohibits ambulance builders from disconnecting power to the vehicle itself when this switch is turned off. However, this switch probably kills everything on yours considering the year of manufacture.
If you have a true Dual Battery System, you are dealing with two distinct systems in addition to dual batteries, (1) one being the
charging system which includes the alternator and the Battery Isolator or ACR, and (2) the other being the
discharge system which includes the Battery Selector Switch (if you have one) and the Vehicle Fuse Panels and Rear/Accessory/Emergency Load Panel. Don't confuse the term 'two systems' with the term 'dual battery' system.
A Dual Battery System can consist of two individual batteries, or two individual banks of batteries consisting of two or more each. I believe you said you had three batteries connected presently, right?
I think the first step is to confirm exactly how each battery is wired in relation to the others, or to what devices, and then we can go from there.