I just redid the vacuum lines on my 2000 S so this is still fresh in my memory. Your diagram in post #4 looks correct for our year. I did notice from reading on this subject that there are differences between engines in that sometimes there is a 4 way connector and sometimes two 3 way connectors but the components are the same and they are all connected one way or another.
Looking at your original photo obviously the right branch goes to the vacuum canister, the left one goes to J for the flapper valve and I assume that the top one is the line that you traced back to H and then to the plenum... so the final branch should go to E which is (in your photo) behind the vacuum canister. It is the hardest one to get to. You can get to it by removing the alternator or the plenum (I would guess, my engine was out so it was a lot easier).
My suggestion is that since you will have to be digging around in there that you renew the vacuum lines and verify the vacuum canister. The stub of vacuum line looks too short the be connected to the change-over valve, I would guess that it is broken the same as mine was, the original materiel gets brittle with time.
My vacuum canister was leaking as was the canister on the failed engine that I have laying around, so chances that yours is leaking are pretty good. My experience is described in post #49 of this thread:
Bought a 2000 Boxster S project.
This video may help you...
https://www.youtube.com/watch?v=7OLakpX6Yj8
Boxster
Hybrid Mode
