Kaleb,
Where you might be going wrong is your machining procedure.
You must have both parts screwed together BEFORE drilling the hole for the piston rod. If you don't do that, the two parts, being made at different times and machine settings will almost be guaranteed to be out of concentricity with each other, especially if they are a threaded pair done with taps and dies. Stuffing glands are usually made as a matched pair, purely for that reason.
In fact to do it correctly, you should have the stuffing gland fitted to the cylinder bottom, then the cylinder fitted onto a trued up mandrel, finally the piston rod hole is drilled. Doing it that way, the bore and gland will be perfectly in line, allowing the piston free movement up and down without being forced onto the sides of the bore by an out of line gland to bore.
Bogs