That line on the side there that you have plugged is just a vent. On my 1980 a black vacuum line leads from it, through the firewall, and into the cabin, right there underneath the steering wheel. It goes to nothing. It is attached to nothing. So you can leave it open, not plugged.

I think that you still had bad shifting with the main vacuum attached directly to the transmission's vacuum line is because it doesn't always have full vacuum going to it constantly.

You said that you have a lot of stuff plugged in the engine compartment. I can't really tell you what to do except keep on trying/troubleshooting, but try putting everything back to normal unless you know that something is leaking (and should be disconnected).

For example, it would probably be good to disconnect and plug the line that goes through the firewall to all the door locks, fuel flap lock and trunk lock, etc, and just use the locks manually for now. It might also be a good idea to disconnect and plug the line going through the firewall to the ACC (should be green w/ yellow stripe).

Again, from here I can't really help you too much as it is all just troubleshooting. Do you know if the transmission fluid/filter have been changed? Maybe that could be a cause of your shifting problems.

Oh, and if you haven't already, try sticking a bb (ball bearing) or some other type of plug in the rubber portion of the hose that attaches to the EGR valve (under the air cleaner). That way, you can be sure that if the EGR valve is bad, you aren't loosing vacuum from there (and you might also pick up some more power and MPG's ). Although I'd recommend you get your shifting straightened out before you plug the EGR.