There's two vaccum nipples on the passenger side of the intake. I think the upper nipple is for the vaccum line that comes out the wiring harness. But the lower nipple, where does it connect to? I'm thinking it connects to a little solenoid looking thing near the EGR vavle. It is on a bracket adjacent to where the fuel lines intersect the fuel rail. I see a nipple on that "thing" and I figure a vaccum line runs between the lower intake nipple and that one.

I took the intake off to reseal it and this vaccum line is just... gone. And my memory isn't serving me correctly. Can somebody verify this?

 

The lower nipple is the connection for the vacuum line for the fuel pressure regulator , and likewise the "thing" you're referring to is the fuel pressure regulator itself. You're correct in that this lower intake nipple does connect to that device.

 

http://shbox.com/1/fp_reg.jpg