You did good. Pretty common to have to clearance the main seal cap for the stud and 12-point nut. Just looking at it when you fit it up tells you, "Jeez, I gotta file a little bit here." I've even had to machine on the provided main seal cap to clear #5 main cap on $5,500 aftermarket aluminum blocks. Nothing comes perfect. You just gotta be smarter than your engine.
Dad always told me, "Look at the problem Jimmy. It will provide it's own answer."