I honestly don't think it makes a difference if rear dist port is open or capped, BUT I won't argue the point as it just makes sense to for it to be able to "breathe"... More trouble to connect a vacuum pump to front and read timing with/without than it's worth...
I have two lines going to the Automatic Transmission. One is the metal tube direct from the ported vacuum manifold. The other is tied into the carb dist port although the diagram shows it should be tied into the EGR port. Looks like someone may have switched things around. What does this second line do? The car shifts fine now so I am hesitant to move this line over or block it off.
The best that I can remember I had two vacuum lines from the engine going to a 'F' fitting on the firewall...two "IN" and one "OUT" going to the transmission. I took it that Ford wanted to be sure that the transmission was getting good vacuum
