I don't remember reading it but are you sure that the ring on the balancer hasn't rotated? Mis-timed engine could explain much.
The 4v 351-c balancer is notorious for it.
You could try advancing the distributor until the engine smooths out. You could be running now up to something like 45° retarded. Having the outer ring rotated out of sync won't imbalance the engine significantly. The counter balance is on the inner hub. The balancer could have rotated since the time you ran the engine on the stand and the time you started it in the car.
Those things are just "glued on" and with age the glue dries up and fails. If the glue has dried up just the inertia of the engine starting up can shift the ring. Then you would be timing the engine to the wrong spot even though the markings would indicate they are correct.