Issues with my 2001 F-250 7.3L transmission continue...

Glad you got it fixed!! You definitely need an alignment after the ball joint replacement, and surprised they didn't do that as part of the job. Biggest effect is going to be accelerated tire wear, and possibly pulling to one side or hard to keep pointed in a straight line on the hiway. Depends on how far out of alignment spec it is. If it's uncomfortable to drive, I would get it aligned now rather than wait. If you can live with it, then wait until you get new tires,.