Paul,
From my experience, the 4R100 is a pretty reliable tranny. I can understand your confusion about the correct fluid, the last time I bought some Mercon from Ford, they seemed to be somewhat confused, too.
I think you'll be all right with a complete fluid change as your tranny seems to be at least working. It may be that the Dex/Merc has allowed some build up in a valve seat or has caused a sticking valve. The new fluid with it's additives should clear it up. If not, you might want to try some tranny additive but I would hold off for a number of miles for the new fluid to work.
I've forgotten exactly how the strainer is in that tranny. IIRC, Ford says not to replace it under normal conditions. You may want to shoot some solvent up into it and blow it out when you have the pan removed. Then again, you're Ford's customer and they should be willing to give you some advice on the filter and the procedures you're using.
I know you can run the fluid out of the tranny by removing one of the coolant lines and running the engine but don't use that procedure for mine. There are videos out there that show how to do it. What I do with mine is drain the pan about every 6-8 or so oil changes and add back in new fluid. I aim at a 25K mi interval but don't always hit the bullseye. This replaces about half of the tranny fluid. I figure by the fourth time I did it, I had pretty well replaced the old fluid by dilution and the transmission sees new oil at that closer 25K service interval.
