M103 Intake Mystery Vacuum Port
 

It started misfiring on the back cylinder (closest to the firewall) and after checking spark and fuel noticed an open vacuum port on the intake manifold of the back cylinder. When I covered the hole the engine started running on all cylinders. I looked all over, with a mirror even, and saw no sign of a mate. I have the service CD and couldn't find anything other than a background indication.

Where does it go, what does it do (if anything)?

Look at this article:

http://www.peachparts.com/Wikka/M103VacuumLeak

and page down to step 2. There is a picture of a vacuum line for the EZL and does it apply to your car?

That doesn't apply but further down a picture does, kind of. It refers to a vacuum line that goes to the automatic transmission, but I don't have that option. I guess there was just a plug that fell off, which is almost too easy to replace.