Any Ideas?

I changed the alternator in my 68,and now it runs like crap.It's really flat and stumply and backfiring.I checked the vacuum advance,it's fine.It seems to be firing on all 8,I also put the old alternator back on and no change.I am running a Pertronix ignition,do you think the module is bad?Any ideas would be appreciated and thanks in advance.P.S. the alt is the internal reg type.