I'm planning on doing the SE comp upgrade but I plan to throw on a chrome inner primary at the same time. If you read the instructions in the service manual, it states to remove the inner primary before you remove the stator cover. But if loosening it works, then all the better.
Years ago when I worked on cars and trucks, on the small block chevy, when we had to pull just one head we would pull the intake bolts on that head side, then loosen the other side and pry the intake up slightly and wedge a punch under the end rail to hold it up. Would shoot some liquid sealer in the end rails before installation and a new gasket on the one side of the intake then slap on the head, torque up and pull the punch, fill the gap with sealer and put the intake bolts in and torque up. It always worked without leaks.