The issue you're having is why I like to leave std port openings actually "std" size on heads without raised runners(heads that will use the valley pan gasket).
It's also another reason I prefer to use raised runner heads if possible....... Just to get away from the valley pan gasket!!
68 Satellite, 383 with stock 906’s, 3550lbs, 11.18@123 Dealer for Comp Cams/Indy Heads