Had the same issue recently - shaft would not fit even before the seals were installed... I measured the shaft and if I remember correctly, it was .250". Ran a .2505" reamer through, still tight. Then ran a .2510" reamer through the carb. Everything fit after that. I can't recall what the original shaft measured, but will check later and update.
It appeared to be a simple tolerance stack up issue between the carb and the new shaft.
EDIT: Measured the old shaft, it ran .2490". Moreover, I remember the reamer telling me the holes on each side of the carb were not aligned axially - as if IH drilled the holes from each side. Sure enough, the choke shaft has an uneven polish pattern indicating the holes were not perfectly aligned. No measurable wear on the shaft, however.