You mean the alignment dowls that are on a couple of the bolts to guide pieces together... like a roll pin with no seam?
Yes, those can be a bitch. I usually leave them in place if they don't come out easy and just clean them and around them with scotch-bright, rub them with some grease to reassemble. If they are buggered to the point they need replaced you can put the largest size drill bit you can fit the shank of it inside and then grab them low with a set of dykes (diagnal cut pliers) and lever them out.
You may have to start with a smaller drill bit and wollow (technical term) it around to straighten them out again to fit the next size in... Also you want to put something under the head of the dykes, like a popsickle stick, when you use it like a lever to protect the gasket surface.
