Your intake ports won't be changed much with just .040 taller head gasket. Probably about a 1/32 difference in alignment. What I'll have to do is check to make sure my intake doesn't bottom out on the ends. I only had .015 when the head gasket was .040. I had to mill about .030 off the ends so that I could run a 1/16 intake gasket. It may allow me to run the 1/8" thick intake gaskets. I'll just have to wait till I get them on to find out for sure.