On close examination of the wires going to the Options d-sub connector, I noticed that I had reversed the connections of RZ194 (Pilot) and RZ195 (Co-Pilot) harnesses with the RZ943 and RZ942 harnesses. Their respective pins were also reversed in the WH-00026 Options d-sub connector. Repositioned the pins in the connector and cut the wires at the butt splice connections and reconnected them (via new butt splices) in the correct orientation. After this wiring correction I'm no longer getting continuity in the Nav/Strobe switch. I hope I have corrected the short circuit problem for good.
Removed the blue vinyl film from the right Flaperon.