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).
I'd be inclined to remove that bolt and then get the remains of that guide insert out completely - and replace it - as it's there for a reason.
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!I'd be inclined to remove that bolt and then get the remains of that guide insert out completely - and replace it - as it's there for a reason.
Weird.
Steel or aluminum? File away.
Maybe you can drive it out with a drift from the top?
Just for kicks have we actually taken the time to check if the numbers match on the cover and head?