Like I said, it would be hard to screw it up, but I'm sure someone has. Just making darn sure. It would be easy if you changed timing chain/gears and could see what's going on, but if it felt "springy" and wanted to push the top side out when tightening it down, then it sounds like it's in right. Besides, that's probably at least partly why they put the sacrificial stud up on top, besides clearance issues. So you don't ruin the threads in the block when trying to draw the pump to the block against spring pressure.
Fix what you have first, and have something to drive while you build a new engine.