not sure I have the total picture on whether you used the cork end gasket or not. When you "dry" fit the manifold with the manifold just laying on the side gasket, if the end gap is greater than the thickness of the cork gasket, you may need some rtv on top of the cork gasket if it's not going to "crush" when you tighten it down. If that is so, you will need to glue the end gaskets with something like High Tack (use brush-on type to avoid spraying it on stuff you don't want all gooped-up) or 3M "gorilla-snot". Follow directions on the packaging.
The pins can just be roll pins, available at a good hdwe store. Did somebody remove them? Some aftermarket manifolds don't have locating holes, that's one of the reasons they are removed.
