Thanks Gelbster! I'll post some of it here to make it easier to find:
First, let me explain, there are a few separate systems that use vacuum from the intake. The most common one to fail is the secondary air injection system. That is the one I replaced. The other vacuum users are the brake booster and the fuel pressure regulator. Both of these looked good, so I left them alone. ***Tiptronics have a vacuum line that goes to a valve on the transmission. 2.7L and 3.2L engines have a vacuum line that goes to an actuator for the flapper valve on the front cross tube.***
This diagram shows the simplest system: 2.5L manual trans.
SAI vacuum system:
***This is for U.S. cars, the SAI was not used in R.O.W.***
The SAI is an emissions system that pumps fresh air into the exhaust for the first minute or two after a cold start. Common DTC codes when there is a vacuum leak in the system are p0410 and p1411. A failure of the SAI system will not damage your car, but a vacuum leak may cause the engine to run lean and lead to other problems.
-Remove the throttle body and cross tube for access to the rear part of the system.
-Remove the alternator for access to the front part of the system.
-Pull out all the old tubing.
-I replaced all the tubing, but reused the check valve and Y.
-Put it back in connecting to: 1) Electric change-over valve. 2) Vacuum source at cross-tube. 3) Vacuum resevoir. (2.5L 5 speed models have the simplest system)
***recommended: Also replace the small tube that connects the electric change-over valve to the vacuum powered change-over valve.
-Reassemble everything else that was taken out.
Old:
New:
The video (Currently some sections of the forum allow videos to be embedded, some don't.):
Resonance flapper connection, 2.7L and 3.2L:
There are some other posts with good info scattered across the forums that we can collect and repost here:
-Brake boost vacuum line connects to right rear intake on the Tiptronics and the line includes a venturi.
-Brake boost vacuum line connects to the left front on the manual cars.
-Details about the flapper on the 2.7L and 3.2L.
Edit 5 Sept 2016: Added diagram showing resonance flapper connection.