If the new spindle spins, has the pulley inline with the other pulleys and the pulley is the same diameter, it's not the problem.
It's possible there was a missing washer/spacer on the pto assembly, as you saying the bolt broke off flush with the pto shaft, and the remains of the bolt in your hand only shows a thread or two which is a little too close to running out of threads for my liking...
I don't know why the new pto clutch failed, perhaps it wasn't assembled right, perhaps the bolt wasn't torqued right, perhaps the bolt just decided to fail, perhaps something else.
Going forward, I would suggest
-putting on a new pto with a new bolt the correct length, and with the right spaces/washers
-torque the bolt down
-with the belt still off, spin each of the spindles to make sure they rotate easily, and check that the blades are installed properly and not bent/damaged (as you mentioned the deck was vibrating more than usual)
-put on the belt and feel the tension to make sure it's not too tight, check that the belt isn't rubbing on anything, and manually pull the belt to make sure it moves (this won't be easy, as there is a brake in the pto clutch that means you need to put in some effort to do it)
-start up the engine, and have someone sit on the tractor and (over clean pavement to minimize blowing debris) turn on the pto while you watch how everything spins from a safe distance off to the side, to see how everything works and if anything is wobbling.