I had an exhaust manifold stud out and sprayed brake cleaner in the threaded hole circled in green. To my surprise, the brake cleaner flowed out of the port circled in blue. I thought the stud was in a closed, blind hole. I also could see carbon deposits on the back of the stud. Does this mean the stud hole was drilled too deep and got into the exhaust port or is this normal for a 22RE head?

 

What about the two on the third exh port? Same situation? If so i would assume normal.

 

I'm not sure, I just pulled this pic from the internet. I didn't have those studs out at the 3rd port.

 

Those ports are part of the EGR system, they direct exhaust gas back through the back fo the head, through the EGR cooler and over the the EGR valve. I've never checked if those studs go that deep, but they would seal up the hole. Video below talks about the LCE Street Header specifically, but describes those small exhaust ports: