Thank you for the reply!, I am sorry I forgot to post this...I have tried it with the air filter off as well as on.
I have also use the ultra grey permatex sealant to seal the case (which might have been a mistake...I can't seem to find yamaha bond anywhere...) and I used permatex red high temp gasket maker to seal the cylinder and the high compression head I have 2 gaskets on the base cylinder and 1 metal gasket on the head.
I tried it without the head gasket and it hits the high compression head, but it clears it just fine with the gasket.
I will try to post pics of my porting job, just for that to be analyzed.