At times the guide rods can be slightly out of alignment to each other. I have noticed that each pump kit is a bit of its own beast.
Tweak the small guide rod if you have some rub and see if that helps.
It sounds like the bottom rod is slightly out of alignment. This would make sense as the bottom rod is threaded and thus depending on where the rod finally rested on the teardrop plate it could be slightly out of alignment and need a little tweaking. I have done it on nearly all my pumps to make them perfect - but I am anal.