Follow post #6. Print that out and take it out to the car with you. Deleting the ARV and EGR controls will greatly simplify it.
When I picked up my car, I had the same nightmare under the hood. Once you get out there and start chasing lines... It is pretty simple (you will be surprised how simple).
The line from the top off center of the saucer with the green dash pot goes down to the trans. and the other goes to the vacuum source (if I remember correctly). On the bottom of the saucer... The center line goes to the ALDA and the one off center goes to a switchover valve. I'll see if I can find a pic and post it up here for you. Or PM me and I will e-mail you a VERY high res. photo.
Also, be sure that the lines coming off the "main vacuum line" are coming of and going to the right places before and after that check valve in the main line.
EDIT:
Here is a pic before I removed the EGR and ARV controls:
http://i247.photobucket.com/albums/gg133/litespeed58/Drversside.jpg
I can put up a newer pic after I deleted the EGR/ARV if you need it. But, the engine bay is not as clean anymore.