DAVE S. - That's the biggest problem with the cast end decks...all three spindles mounted in those large pieces of CI. The next model newer decks with the open ends like on the 72/104/105 etc. used three identicle three-bolt spindle housings and only a CI pie-shaped piece in the front center section.
Dudley is correct that You'll need to use force to basically warp the steel stamping back into shape to align the blades. A large flat washer or two between the blades & spindles will correct a small amount of misalignment. You may have to use a series of blocks, jacks, a press or something to get the blade mounting surface of all three blades in the same plane. When You get the blades close to lining up spin the blades 180 Deg. so both ends line up the same against the ajacent blade, then spin the next or normally center blade and make sure it lines up the same against the first blade, then check against the last blade, spin the center blade again, then spin the last blade 180 deg. That checks all three blades for straightness and alignment. Spindle bearings must be tight also, they need a little freeplay or clearance or they overheat and ruin the bearings & seals.
Also make sure Your deck is hanging level after checking air pressure and equalizing in all four tires to the recommended pressures.