Yes there is a gasket inbetween the intake manifold and the throttle body. When I cleaned my egr ports the gasket ripped on me and I had to wait to order a new one from mazda cause air was getting through and causing an idle problem.
Yes I did have a noise it had a sucking sound coming from the TB and my idle was pretty messed up, but since you had clogged EGR ports and now they are clean you have to give the ECU time to adapt and learn about the air/fuel mixture.
Okay this is what I would do, if the current gasket is still in one piece I would go buy some RTV gasket maker and put it on both side of the gasket then while your TB is off clean the ports a bit more and tighten those four bolts nice and tight. This would really seal it up you only need a very little bit so just smear it evenly in a very thin layer. If the noise it still there then it has to be something else.