I caught a tree stump last week, and bent a blade on my 54" mmm. Had new blades ordered, and put them on. The right blade still wasn't level. It was about a half inch higher than the middle blade when I would spin the blades around to see if they align. It is also off on various locations as you measure its height compared to the other two. The middle and left blades are consistently at the same height.
So, I took the deck off and took apart the right spindle. Found a crack in it. The bearings and shaft in the middle seem straight, and it doesn't vibrate, but I am replacing it due to the crack. Hopefully that is the leveling issue.
This is an image of how the right and middle blade align. Better now that I took it apart and re assembled, but still off.