I couldn't wait for the silicone to set, as I said I need the car later today.
StreetRod and somebody else said that the 3rd pipe goes nowhere, that didn't sound right because Ford wouldn't have put it there for no reason; I guess it must be a pulse damper.
Anywho, that's all I needed to to try something else: I found a convenient piece of rubber hose in my BMW parts stash and cut a likely looking section out of it. It was bent in almost exactly the right angle.
In it went and everything runs perfectly.
The idle is good, the off idle transition is good.
I'm not sure if I'll even put myself through the trauma of installing the repaired 3 way part, we'll see.