Hey there Jess, Have you replaced the cap and wires yet? I know they were not new when I sold the truck, and they will cause exactly the symptoms you are describing. The moisture will build under the cap or condensate on the wires and cause arcing. Pop the cap up when you know it will act up and see if there is any moisture in there. You can also run the truck in the dark when it is acting up and watch for arcing from the wires (you may have to have an assistant put it in reverse for you while you watch).
I never did move the ECU, As I recall it is behind the right side kick panel / glovebox area on the 1994, 1995 and under the hood when the trucks went distributorless in 1996.
On a side note, the water in the floor is fairly common, usually from the windshield seal, sometimes through the HVAC system. I do recall it getting wet there sometimes, but since I've had the truck well over the lower seals on occasion I didn't fuss too much with it as it was not too bad then.
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 Mike Mason
If it's not leaking, it's out of oil
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