First off I have never done a pinion seal on a ford. I used to work in a GM garage. But I have done them on many GMs and a coupld Jeeps.
On every one I have ever done I mark the nut, the pinion shaft, and the housing at the same point so when I tighten everything up, those lines match up. I also count the number of threads showing between the nut and the end of the pinion shaft and note if there is half of the thread showing or the whole thread. You will also notice you are getting close because when you reach that point, the nut will be very hard to turn by hand. I use impacts to remove and install if I don't have the yold holder and my breaker bar.
I know this isn't the 100% correct way to do it but I have never had one come back.
Just my $.02