The first connector is a "pass-through" connector. It allows signals and power to pass from one side of the firewall to the other. It is not the brake controller connector.
The second connector is the usual color (brown) for a brake controller connector. But the wire colors don't seem to match what's shown in Ford's documentation at this URL:
According to the diagram on page 268 (that is, the first page of the PDF file) at that URL, the brake controller 6-pin connector has the following wires (on the harness side):
Light blue and black - 12V
Light green - brake signal to electric brake controller
Dark blue - electric brake controller signal to trailer hitch socket
Brown - Headlamp switch
Black - Ground
I don't think there's a third 6-pin connector under the dash, but am not sure of that. I am sure your coach has a brake controller connector, so no splicing is required. I have to load a DVD on my computer to bring up the E-450 harness wiring diagrams. I'll do that and report back what I find.
I assume you plan to tow a trailer with electric brakes behind your motorhome. If you plan to tow something different, please let us know.