If you look at the splines on the PTO side of yur shaft you will see that they end a little premature for proper Avis driver alignment.
What this means is you will want to lathe out some if the outer splines inside your PTO side driver. Say that again slow,
outside splines on the
inside of the PTO side driver. You will see a smooth surface inside the driver now, the spline cut doesn't go all the way through. You just need to increase the depth of that smooth area inside the PTO side driver by 1/4" - 3/8" if I remember right. Give Avid a shout, they are aware of the issue.
Then you can take measurements from the tunnel sides and center to center on the track windows to get the extros set square in the windows. You will end up moving the mag side driver in toward the center by the same amount you move the PTO side driver out to keep a proper center to center. I hope all that garble made sense, if not, pm me your phone number and I'll give ya a shout. I type really slow, I started this reply day before yesterday. LOL. Good luck. EW
EDIT:
Found this pic, you can see how the shaft goes from spline to smooth on the PTO side. Problem is the splines in your drivers aren't letting you press the driver onto the smooth part of the shaft, hence the need to lathe out some of the splines inside the driver for proper alignment. Hope this is clear enough. EW