If you're doing ball joints plan on doing sway bar end links(cheap) and outer tie rod ends while you're in there. You may not have a choice since sometimes it's almost impossible to remove the knuckle to get to the ball joints without cutting them off. The biggest PIA is the rear bolt on the driver's side upper control arm. A wratcheting wrench is very helpful here. Also usually it's best to replace all of these parts in pairs.
Why motor mounts? Can you see your motor move?
For vibration in rear...if the tires, rims, balance and alignments are all good. THEN I would look at rear sway bar end links, rear sway bar bushings, and rear toe links. But really I think you will be surprised how much alignment will affect vibration.....But no sense in getting the alignment done until you replace all of those front end parts.(and rear if they're bad)
Oh and make sure you get the right size ball joints. Put your VIN number into Ford's parts website and it will tell you what size. You can't rely on whether you have a sport/non sport or what year if it's a gen I.....trust me. It has more to do with when the car was manufactured.