Double check the firing order on the cap

I think that's where the problem is.
We used to have a similar thing happen with U-Hual trucks (460) during a Preventative maintenance when some pinhead changed out a cap and rotor sometimes, and I can't remember exactly which they would reverse. PM'd a buddy who has my old job there, if he texts me back I can tell you which ones.
HMmmm, I would have bet money the 460 was a neutral flywheel delio (I don't do Fords).
Was the old one weighted?
GT
460's are, for the most part, internally balanced, and the flexplates will only go on one way (Hole spacings force this)
Ray
Edit: Sorry about the pin head comment, wasn't directed at you. The guys who used to do this routinely did this 5 times a day every day and even the mechanical bays would miss it and it would end up in one of my QC bays to diagnose and fix it. You don't do this anywhere nearly as often and is an easy thing to do. Sorry if that came off the wrong way, I'm tired, lol