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I don't think a mismatched head and top cover would have alignment issues where you are but rather where all the holes a line bored between the bolted together halves (bearing holes, valve cover holes).
Pulled off the head yesterday and gave things a closer inspection and it turns out that the portion that is slightly protruding is a steel insert. Think I'm going to hit it with a hand file until it's level across the entire surface.
Agree on removing the broken guide "hollow dowel" out and replace with good part. Might be that because it in damaged it is causing the cover to not line up right or distort when the bolt/nuts are tightened!
Yeah, the engineers designed two alignment inserts to help keep the head and cover situated properly, that appears to be the remains of one. I'd be inclined to go with those slide rule Saki jockeys of old on this one.
Other opinions may vary.
If you look at Gary's head and cover pic, there shouldn't be a locating dowel in that spot. It should be in the hole on the other side of the cam sprocket. If possible, I'd remove it.
Bottom line is it shouldn't be there. That hole should be just all aluminum. Maybe someone tried fitting a dowel there without success. It wouldn't go in all the way because the hole is too small. Maybe you can drive it out with a drift from the top?
Thought about that. Not sure if there is a lip on top so pressing it out from the bottom would be the way to go. However, by the time I find a drift or turn something down on the lathe to press it out its easier to just filing down flat. Its not hurting anything. The stud passes through it fine.
I worked it with a hand file yesterday until I have a nice flat surface, using a flat square to ensure it was flat. Reinstalled the head and valve cover and did a test fit tightening down the head bolts and everything seems copasetic and the rocker arm that was previously binding was moving freely. I'll snap a pic and share it with ya'll if I think of it.