If this was anything like the trouble my 1991 Ranger gave me with the same overnight battery draining symptoms, find both the EEC and fuel pump relays and replace both of them. Even when you take them off, if they look OK, throw them out and get new ones. They're like $20 Canadian to replace. On my Ranger, they were underneath the distribution block on the right hand side of the engine bay. One had a green connector, the other had a black connector. The relays are exactly the same, and should be replaced every year, they are known to stick and do this.
I fooled with everything I could think of in the engine bay related to the battery and anything that might drain it overnight until I figured out what was going on. It took me two years to figure this out because it would only happen during cold seasons, during the summer while it was warm, the battery would only drain low enough that it would still start the truck. So if I were you, this would be the first thing I would try. Also, this problem is related to a lot of Ford vehicles around 1989-1994, if you do a search on the internet, you should find some information on it.
Good luck Sharky