OK, I may have found some help in my 1990 engine service manual.
There is a schematic of a fuel evaporation vacuum system.
It has some parts similar to what you described.
I'll try to describe it, my scanner is dead:

1. Throttle body or air intake has two vacuum ports on it as you described, upper and lower.
2. 50 degree C thermo valve (red) has two vacuum ports on top, and appears to screw into something (the head obviously). Port A is straight up, port B is canted about 30-45 degrees.
3. Purge valve has one port in center of side A, two ports in side B.
B-1 is in the center, B-2 is near the edge.
4. The diaphram appears bigger than the purge valve. It has one port on top, side A; and 2 ports on bottom, side B.
B1 is in the center , and B2 is near the edge.
5. the charcoal cannister has 3 ports: 1 in the center, 2 near the edge, and 3 near the other edge.

OK, let's hook those babies together with vacuum lines.

1. Upper throttle body goes to thermo valve port B (the canted one).
2. Lower throttle body goes to purge valve B1 (center).
3. Thermo valve port A goes to purge valve port A.
4. Purge valve B2 goes to diaphragm A.
5. Diaphragm B1 goes to canister port 1.
6. Diaphragm b2 goes to canister 2.
7. Canister 3 goes to the fuel tank.

If you draw this out, all the vacuum ports should be connected to something.
There will be 7 vacuum lines, including the line to the tank.

Maybe this will helo; that's the only vacuum routing I found in the manual.

DG