Not much of an expert, I've only changed two or three. I don't think changing the valve would have any effect on alighnment.
One thing though is that because of the large diameter thread and the relatively small diameter of the relay rod and the vavle body, screwing them back on can be difficult if you need a lot of torque to screw them back on. Cleaning the threads on the relay rod with a die is a big help. I was thinking about cleaning up the threads of the valve body with a tap, but I didn't have too. To clean up the valve body threads, I used a dremel tool with a small rotary wire brush. There was some sort of junk in the treads....probably left over when the remanufacturer hot tanked the valve body.