I would get rid of the breather and stick with the PCV. The breather is just a vent, the PCV system has a small about of vacuum that evacuates the pressure in the crake case.
Sometimes when doing it by hand they won't move, I recommend once you have the tire off the ground, place a prybar under the tire and lift (you don't have give it alot of force). I replace them if there is more than 1/16" movement.
You should allways clay the piston to check for PTV. Even if someone has/had the same parts, this does'nt count for differences in factory machining, deck height, gasket quench, and how the cam is timed.
Stock pushrod length with new rockers and valves? Did you measure for length? Valve train geometry could be way off. And you didn't say anything about valve springs. You didn't use the old stock ones did you?
Toe does help center the wheels, but caster is what primarily centers the wheels. Stock suspension in fox's have very limited to no adjustment for caster and camber, this is why caster camber plates sell like hot cakes.