My area of expertise is 91-94 Explorers so I don't have the exact answer you want, but usually Ford power distribution boxes/fuse panels are held down in only a couple spots and not too hard to get loose without removing any wires. Check on the Explorer forum for your answer - those guys know...
Was the car originally a 4 cylinder or 8 cylinder? If so there are various pin differences in the harnesses and if something was jury-rigged to work it may have let go. I worked on converting a 4 cylinder car to a V8 recently and the two immediate issues I ran into trying to use some of the I4...
If you are fixing it to sell it, I'd suggest going the easy route of swapping in a used junkyard E4OD. Many people will hesitate to buy a vehicle that has been modified with powertrain parts that are not stock (obviously besides a performance build).
If you are set on a Powerdyne unit you may need to look for a reseller. Online speed shops may have old stock if a company has recently gone under (or maybe Powerdyne only sells through them, not direct), or try eBay.
Sounds like you have a loose connection somewhere or possibly even a loose ground wire jiggling around. Is the battery strapped down tight? Check all connections for play and even check on weatherpack type ones that the retaining pins aren't broken. A connector with a loose pin could be shifting...
I don't have the exact answer you wanted, but keep in mind you can purchase grommet kits from any parts store and drill your own hole wherever you want.
Also on the sway bar issue, consider starting with all new bushings - it should make a big difference even with your stock bars. Given that you don't daily drive it you may be happy with poly bushings, which will make that sway bar perform a lot better.
+1 on LMR (LRS). Personally my favorite cheap upgrade was subframe connectors. Made the car tighten up a lot more; no more squeaking over bumps.
As for suspension, my 90LX came with Eibach lowering springs. I hated the ride and got a full set of new stock replacement MOOG springs. Huge...