WillsLimo,
I will hazard an opinion...the holes go DOWN. I think if you look closely at the shafts, you will see much more wear on the bottom, the side with the holes. This is an effect of the various components trying to push the rocker arm up.
I have cleaned these shafts before. They can be difficult to open up 100%. I think I remember driving the plug out, reaming and cleaning until no crap was left inside. A bath in carburetor cleaner would be the cats meow for this situation.
Stuart
