Mark, my machine is the same model as yours and my Y axis rails were off in parallel by quite a bit. The hardened rails shouldn't wear out to that degree with the kind of use you mention. What I did was to first make sure that the top rail was flat, no dips etc. with a straight edge, then checked it for parallel to the table surface as best I could. If your table has been surfaced with it out of alignment, you can't use the table surface, but can check with a straight edge laying across the X rails. Once satisfied with the top rail, check the lower rail for flat with the straight edge and adjust if needed by loosening the small screws holding the rail to the aluminum bar first. If you can't get flat with those, then you can tweak more by loosening the cap screws on the aluminum bar and gain a bit more. Mine were flat, so I just loosed the lower rail cap screws that hold the aluminum bar with v-rail on and using some spacers of the same/proper length, clamped them in place between the inside edges of the v-rail, not the aluminum bar, and then clamped the lower rail in place from top to bottom and then tightened the cap screws a little at a time working from the middle out. You can gain a little spread by loosening the cap screws so you should be able to get the eccentrics to snug up afterwards. Be sure to loosen them before spreading the rails apart. A little blue loctite may be a good idea on the small rail screws if you loosen them.

Some oiler/wipers for the rail is a good idea too as the older PRS tools had none.