DO NOT REPLACE THE GUIDE PINS WIH BOLTS! They are there so the long end runners can expand/contract slightly with temperature changes. Bolting them down solid can result in the intake warping and/or cracking. If you're firmly convinced that you're smarter than the guys who designed the engine, the pins can be removed with plenty of heat, penetrating oil, and vise grips. They're 3/8-16 thread like the rest of the manifold bolts. If someone has milled the manifold mating surface to straighten the face of it sometime in the past, it's possible the alignment rings are a little too thick and the manifold is bottoming out on the rings before it clamps the gasket tight. Don't remove the rings- - - - -just shorten them a little with a file or a disc sander.
Jerry