Where are you looking for a brake controller line? Pigtail where?
For the Minnie and Itasca Spirit that era, Winnebago did not run a brake controller line from the cab to the trailer wiring connector. Also, brake lights are not separated from turn signals, so that a brake light signal can't be tapped to provide a signal to activate an independently powered brake.
Diagram for the six-pin connector is on page 6-9 of the 120 page 2003 Minnie Owner's Manual (available free as a PDF under Resources/Manuals at the Winnebago site0.
Pins are, clockwise from notch, on the wiring side of a six pin plug you would build:
TM = tail lights and markers (at the notch)
GD = ground
LT = left turn/brake
RT = right turn/brake
S = unused spare
A (in center) = backup lights
These letters will be found on the face of the matching connector packaged with the manuals from Winnebago. An aftermarket 6-pin might be marked differently.
This wiring is really for pulling a towed motor vehicle, rather than a trailer. Six-pins for trailers might be wired differently. For this reason, an aftermarket 6 to 7 adapter might have been made using incorrect assumptions. For that matter, I don't recall the six-pin round being used for trailers, there was a six-pin bladed connector for that, before the seven pin came into use.
If you are pulling a trailer with electric brakes, you would do best to install the 7-pin trailer wiring connector, using the four useful lines from the 6-pin (TM, GD, LT, RT) and running wiring for your brake controller line and trailer charge line.
Power points designated for these these two purposes are included in one of the under-hood junction boxes of the E-series (look in the E-series owners manual), but you may have to install fuses or breakers and relays for these high amperage connections, as they don't go in at the Ford factory unless the chassis shipped with Ford's trailer towing package. Similarly, without the trailer towing package, you might have to run a line from the box to the cab for the brake controller, with the package it should already be a loose connector under the dash.
Tom Test
Itasca Spirit 29B