Runs rough after taking off intake

Hi

I have a 2000 mercury cougar with the 2.5 v6
I had a check engine light on for the insuffient egr flow error. So somebody told me there is a channel on the intake that gets clogged on fords that causes this. But they didn't know where it was. So I took off the intake and then realized it was where the throttle body connects to the intake. So I cleaned this out, because it was totally clogged. But When I reassymboled it back and started it, it runs really rough and knocks every once in a while. In park it runs rough and at about 4 to 5 thousand rpms starts to die intermently. I checked all the cables I unplugged and checked all the vacuum hoses.

The only thing I can think is when I took off the intake there was a hose that went from the top of the intake to the master cylinder. When I disconnected that there was a pop and some suction. Do you think that I need to reapply some suction to this?

I really don't know what is causing this and am out of ideas.