As a previous owner of the 5D, and current owner of the 400mm/5.6 lense and used 1DS II. I had to tape the pins of the 1.4 converter to make it work on autofocus on the 5D with the 400mm/5.6 lense and it was slow. Never owned the 40D, so first question is does the 1.4 converter work on autofocus without having to tape the pins on converter? Second question, is it too early to ask whether the 50D will work with 1.4 converter not taped also?
Some of the 40Ds did work going by the internet forum posts, but my 40D did not work with the taped pins. I think the 50D would also not work since Canon probably figured this out somehow.
Only the 1 series of cameras will AF with your 400 and TC which what effectively turns it into an f8 lens combination.
I dont believe the 50D will do any more than your 5D in this regard
With the contrast-based live view AF it should focus. At least my 450D does with 400f2.8+2x+2x (wide open f11) and the 50D should not be any worse than that.