hi in picture 3 with the 3 vac switches, the one on the left, (looking from steering wheel, ie drivers side) is the idle speed control. The one in the middle, and on the right, ( Towards pass side) control the pulse air system,which i don't know if you have or not, if not, just plug those two.
picture 1, that is the main vac feed for the whole system. if you are not using it, definitely plug it, I don't see how your car can run well with that open!
picture 2, the big vac line went to the main feed in pic one, you are correct. the small black "hard" vac line was/is the main vac feed to the 4wd vac system, which i gather you don
't need any longer. the open end of the "Y" went to feed some other vac systems, such as the cto, egr, etc, not sure just from that picture. plug it if not using it, or better yet, figure out where it's supposed to go, and connect it properly. there is a good 84-88 vac diagram available in the eaglepedia. just take your time, identify all the parts, and follow the diagram. good luck, gz