This has been discussed a lot. If you search for "brake controller" [ ------ > ] you will find the threads I think. I will also edit and post links.
http://www.fordtransitusaforum.com/...hp?page=active_topics&ref=&ss=4154j1289510j16
kenjent's thread was for the whole trailer harness, but it gives a good idea of how Ford has made it nearly impossible for the average person to add on things like brake controllers into the rolling computer which the new Transit is. Better to miss the cup holder IMO than INTENTIONALLY buy a new $50k can of worms . . . ?
http://www.fordtransitusaforum.com/towing/10274-installing-tow-trailer-hitch-wiring-harness.html