I have a 99 civic Ex with a B18b1 swap. The car was idling super high on start up and then once up to temp go down to about 1500rpm but ran fine and the rpms would level out even better after some driving. Then all of a sudden sometimes it would drop super low and cut off and then cut right back on. So I decided maybe it was the throttle body bc honestly whoever did the swap did a poor job and it was old. So I got a Skunk2 intake manifold+throttle body combo. Got it all in and I realized that the Skunk2 manifold has an extra port next to the large coolant port on the bottom. The water neck/thermostat housing on the b18b1 doesn't have this. Is there a way to bypass this or not use it at all? Or am I screwed?

Back of intake manifold. The small port to the left is the issue.

Stock B18b1 housing. The center port goes to the larger port in the other photo. To the left it is blocked off.

 

You can block it off. Another option is to "T" it into the "loop" somewhere... pick a location between the water pipe -> IACV -> T/B -> water neck/upper radiator hose fitting on the head.