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That's gotta be the EGR pipe. It'll go through a passage in the intake over to the EGR valve on the other side. I'm not positive, but it might have an EGR Temp Sensor on top? Lots of older systems used those to gauge EGR flow.
Ok, I thought it must have been something to do with the egr but the thing that's throwing me off is that a lot of stuff isn't properly connected on the car. The egr valve is bolted to the top of the intake and there is a nipple sort of thing on the top but it doesn't go to anything. I guess I don't understand how these are connected to each other.
...but the thing that's throwing me off is that a lot of stuff isn't properly connected on the car.
You're probably missing some of the EGR vacuum control hoses. There'll should be a PCM controlled EGR vacuum solenoid in there, too. Drivers side of engine, towards the back.