I ripped it out the other day to replace the large gasket that makes the seal between the plenum and the TB.

I'm wondering how this thing really works. I guess the crankcase fumes, which enter the plenum via the two fat breather hoses, mix with the air that comes from the intake. The oil in the hot fumes condensates in the plenum when it comes in contact with the colder air from the intake. The oily condensation runs down and through that rubber "mushroom valve" to the lowest point of the plenum. The oil collects there in a small chamber and is sucked out through a vaccum hose and into the TB (not sure where exactly). The remaining crankcase fumes will mix with the air from the intake and get sucked into the TB.

There is another vacuum hose connected to the top of the plenum. I have no idea what that does.

Could somebody please tell me if I got it about right?

The orange silicone flap is a bypass valve that changes the flow of the breather gases/solids into the throttle body from the vacuum line at idle to through the flap at WOT. At part throttle and some vacuum there is oil and gases flowing thru both both the flap and vac port. At WOT when there is no vacuum all blow-by solids and gases are entering the throttle body thru the silicone wafer and into the top of the throttle body. Conversely when the car is idling all those same solids/gases are entering thru the vacuum port below the throttle body butterflies. The gases/solids transition from the vac port to the disc as more throttle is applied.

The above phenomenon also creates a problem I have found on EVERY plenum on every car I've had the plenum off of. The vacuum port in the plenum or the throttle body becomes plugged with oily sludge, varnish, coked oil that is blown out of the valve cover as "blow-by products." Doesn't hurt anything as the silicone disc takes over anytime you're off-idle or at zero vacuum. And all the cars I've had the plenum off have had more than 50k miles with many hovering near the 90-100k miles. One cure that goes a long way towards keeping the plenum vac port open is to open it up a little bit with a drill bit. Or use a drill bit the same size as the stock port inlet opening as a great way to clean/ream out the crud... just push a drill bit in and out of it a few times by hand. The throttle body port can be cleaned similarly but DO NOT drill it oversize!! The port into the throttle body below it's brass hose barb is significantly smaller I.D. than the hose barb itself. Clean it with a same-size drill bit but DO NOT try to bore it even a smidge larger!

The vac line you mentioned "not knowing where it goes" is the one I just mentioned in the above paragraph. It goes from the base of the throttle body on the secondary side (drivers side/large port) and exits below the throttle body butterflies. It's routed to the plenum and connects near mid-line on a horizontal plane just a few inches away from the throttle body hose barb it connects to.

The line on top of the plenum is not vacuum. There can be no vacuum upstream of the throttle body butterflies unless there was a tremendous restriction or blockage in the airbox inlet, airbox, air filter, MAF housing, induction hose or plenum intake. As to it's function I'm not sure at this point. Maybe someone else can chime in with the answer on that one.

Thanks for describing how this all works. I copied it to my "file." Now to my question:

The vacuum line that goes from the plenum to the TB was disconnected for at least 6 months. It must have fallen off the plenum. My mechanic couldn't find where it was supposed to go, and the dealer didn't find it either! A couple months ago, after consulting people here on AW, I found where that vac hose was supposed to go, and I reconnected it. My mechanic plugged the hose with a screw, but the TB must have been sucking air for a pretty long time. Do you think I may have ruined anything over time?

No other harm can occur as a result.

Totally cleaned out EGR system this weekend. Port on TB was totally clogged with carbon like UrS4 said. My idle is now the best it has ever been!

Isn't it great to actually find out what's wrong? :-)