i know these kinds of problems. that's why i wrote my own exporters for maya and blender. i wouldn't have had the nerves to continue working with gamestudio without them.
i don't use cinema4d but i think it really would make sense for you to learn COFFEE (shouldn't be hard) and write your own exporter. that would be a much cleaner solution than some post processing tool. maybe you could also make some money by selling it to other cinema4d users.