Hey bud,
when I'm re finishing someones shaft, I tape off the area of the finish and do
my job. If I need to sand off the finish to remove dents then I use a water based poly, the same as some use to finish cues with and do the first 3 or 4 inches of the shaft.
The poly I use for this is for baseboard or hard wood floors. I figure if its tuff enuff for hard wood, it will work on a shaft.
I use a lathe and a soft Viva paper towel but if you're doing it by hand, maybe try a small foam brush. I've had amazing results using a foam brush for other wood work with pretty much zero brush marks so if you're careful, I don't see why you can't do an acceptable job with the poly and a foam brush.
Just tape off the area you don't want to go past and brush right onto the tape. When you get enuff coats on that you are happy with, remove the tape before it completely drys. There will be a small ridge on the shaft that can be feathered out with some fine sand paper.