OK. I have had a similar nightmare with my 96 Civic LX 4 dr. Only one window will work from the drivers controls - left rear. All of the locks are dead. These symptoms developed over a two year period. I finally isolated the problem and hope to fix mine tomorrow. At least five of the wires are broken where they attach to the main door connector. In addition, the insulation on these wires is very hard and brittle close to this connector. I'm going to buy a new connector tomorrow and rewire from the fusebox to the connector. I hope yours is fixed by now.

 

RonJ has given you 98% of the info needed to sort this out. The other 2% are going to come from you and a multimeter.
That document on the master switch test is GOLD. eveyone should save that or print it out for Gods sake!