Do you know how to change anything else over? The vacuum stuff is really the least of your worries--you are confident in swapping an OBD1/OBD2 fuel injected motor into a non-OBD carbureted (or FI if it's an Si) 86 Civic--you'll need specialized mounts and a lot of new plugs/wires?
If so, just take EVERYTHING from the donor car and put it EXACTLY the way it was in the CRX. Your PR4 or whatever ECU you're runnning will most likely be looking for the MAP signal and stuff. Take out the old charcoal can/sensor array and just put the new one in, drill it in if you have to. That 86 most likely won't have all of the emissions stuff that the newer engine will need.