[Cornishman]

If your getting the heads off, having them shaved a few thou' would be a good move. If they've heated up at all then they may have warped slightly.
As for cleaning up the intake manifold (porting) there's good and bad about doing it. The good is, it will improve the smoothness and speed of the airflow. The bad is, there's something to be said for tumbling air, it helps mix the fuel in the air.

 

[Cornishman]

Not uncommon to have them break. If your taking the heads to the machine shop, you may as well have them extract the studs.