So just to be clear, the 2-3 holes punched in the top portion of the running boards that reach up to the top of the frame, and are a perfect alignment (front to back) with the holes in the frame itself, don't actually do anything? The running board holes lay maybe 3-4 inches outboard of the frame holes. Just doesn't seem right that they wouldn't be used but there is no way I can stretch them up there to make them fit. I'll try to post pics later for clarification.
See pics at :
http://s843.photobucket.com/albums/zz356/blatham489/Running%20Boards/Note that there is no room to push the boards farther inboard to match the frame holes without hitting the end of the spring to frame mounts.