Herring,
Switchover Valve ports #1 & #3:
So on the double mechanical "switchover valves" inside the black box that is controlled by linkage to the throttle [#64/#64a]... so I basically guessed correctly that at idle at least ports #1 & #3 interconnect and thus these provide a simple ON/OFF vacuum signal for the EGR system so it is OFF at idle. Just in case you decide to restore your EGR system to full operation, I'm thinking this vacuum signal might also be present at a higher throttle position!
Switchover Valve ports #4 & #5:
Once again it looks like I am at least partially correct. As to the #2 port, I admit that I must NOT claim to fully understand why there is such a feedback line from what I call the "bleeder" side of the VCV [#65]. My best speculation is that at certain throttle possitions, this line provides a moderate-to-strong vacuum via this line as a means to nullify the VCV's bleeding effect through the line that vents under the dash... and thus nullifies a tranny shift under certain load/throttle conditions.

The later models muddy my understanding of such " stuff " even further... and the 1985 CA cars also add another 5 components to the system that are in or related to and accomplish a much more precide tranny-shifter control and feel of luxury!

Your Question now:
Blocking OFF the EGR system - Yes, so long as the #1 & #3 ports are serving only the EGR system and as long as your STATE dose not arrest you and drag you off to jail for not having it hooked up, I would simplify things [at least for now] by putting golf tee(s) in the line that goes to #1 & #3 [just in case] and also the rubber "T-connector" that supplies vacuum to #1.

Closing Sidebar - On both our much simplier 1980 models, I have learned to use the throttle to help me control shifting... and have found with a little practice I can do quite well at this... basically by backing off on the throttle just enough to make for a smoother shift between:
(a) 1st & 2nd gear..................... by feel
(b) 2nd & 3rd............... @ just before 25 mph........... and
(c) 3rd & 4th............... @ ~30 mph and above !
I feel that doing this (1) minimizes wear on the tranny and (2) allows me to drive more for economy by keeping the RPMs down!
For economy, I'm even running 35 psi "all the way round" in the tires!
It's too soon to give a report on any favorable results!
Regards,