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I think what Denny is referring to is this. Apparently on some earlier models, Ford didn't put all the trailer tow relays and fuses in place, they came in a plastic bag in the glove box, along with a pigtail for the brake controller connector, and the new owner was expected to put these fuses and relays in if they wanted them.
I'm not sure which relays and fuses they didn't put in, but based on your original problem the brake controller power fuse was one of them. I think the trailer connector 12V power fuse and relay was the other one. Trailer connector power is fuse 16 (30A Maxi fuse) and relay 39 in the power distribution box.
Another thing you can do, just for peace of mind, is get a test light and check all your trailer connector pins. The cap for the trailer connector should be labeled with the function of each pin. Hook the alligator clip of the test light to the ground pin, then have a helper go through each function and check for power. You should have turn signals, running lights, backup lights when in reverse, a 12v feed when the key is on and power on the brake feed wire when the brake controller manual lever is pulled over.
My relay board only goes to 37 (downloadable one from David). I see it listed as 39 but what gives?My box doesnt even go that high either.What am I missing? I`ll check all pins when rain stops later