My experience is with GM trucks (S-10 platform and full size vans, trucks, and SUVs). The ABS system seems particuarly failure prone on these vehicles (every single one eventually went wonky) so we did disable it on every one as ABS isn't a cheap fix on GMs. On the GMs, disabling ABS (whether you unhook it or the car's computer itself disables it) simply means you loose ABS, the regular brakes still work very fine and for me have been very reliable...I'm wondering if you have actually lost ABS and NEED to have it bypassed or if once the lines are replaced the systems can be reset and back to normal.
As far as your electrical trouble, remember that the battery is still usually keeping power to the car's computer and radio system to maintain those memories, so eventually a hooked up battery will go dead for those reasons even if nothing else (age, corrosion, wiring/cables breaking down) is an issue. I've seen bad battery cables, weak batteries and alternators going bad causing issues, too, so tracing that down is always fun. I've never really had a vehicle set for more than a week, so I don't know how long it'd take for a good battery with good cables, etc to go dead due to computer/radio memory drain.
I think your vehicle is old enough that OBDII diagnostics do not apply (so the cheap scanners at the autoparts store will likely not work). There may be a procedure for Fords involving reading the computer codes with a paper clip like you can the older GMs. The repair manual might have more details, I don't know.
That's a hell of a deal on getting transmissions worked on, I'd say.
I can tell you that while I did not have any problems with early to mid '90s GM automatic transmissions, late '90s and newer have been...problematic for us due to the amount of electronics in them not being tolerant of heat. Adding transmission cooler(s) and changing the fluid on a 40k mile basis has added greatly to reliability.
