This view shows what I'm talking about a little better.
I also noticed that these.....plugs, or whatever they are. Aren't even. I take it that they're the other end of the threaded stud under the breather cover; the ones I removed the nuts from.
This side seems flush:
And this side seems countersunk:
Did I get something out of adjustment when I removed the nuts from the studs that lock the rocker arm shafts into place? Do you adjust anything in there to even up the rocker arms? Does it matter?