Lenny, I'm not sure what "ports" you are talking about. There are no "ports" under the headers, just casting openings where the studs pass through. If the oil is coming around the center area where the timing chain is located; I have seen several tensioner gaskets be installed incorrectly and the oil runs to the left side of the engine under the headers.
I do not recommend the APE studs. They do not expand enough for our application. They then either strip out the case threads or break in half. I would also only install a factory Yamaha head gasket. Cometic has had several issues in the past with their gaskets.
A pictue is worth 1000 words though...that would really help.
Randy - RPM