In the middle of the front and rear rails there is a small pin driven in a hole to locate the intake. Actually the hole in the underside of the intake is much larger so the term "locating" doesn't mean its critical. If you use the end gaskets you need the pin to help hold the gasket in place. Using RTV alone on the ends, removing the pins and cleaning the holes will allow the RTV to create a finger hoding itself.
Those pins should pull right out of the block with pliers.