The next thing that needed to go in were new axle seals. I initially bought seals from Rock Auto (SKF) and an installer from Amazon for like $20. I quickly found out that those installers, which are EVERYWHERE (Amazon, eBay, etc.) don't work very well (in fairness possibly this is an issue unique to the Ford Super 60, as I'm finding several oddities with this axle vs. a typical D60) and I ended up just ruining the seals trying to install them because they do not properly support the seal. The seals are not exactly free either, the SKF ones were about $41 each. Not terribly happy I searched for a better tool and found one at Torque King 4X4. This is by no means cheap, but it is very well made and worked really well. I bought the tool and seal combo since I ow needed ANOTHER set of new seals. Both seals took maybe 10 minutes to get in with this tool, AND it sets them to the proper depth.

Note this is just the setup and the installer is not fully bottomed out yet. The black puck goes flat when it is. Here is a seal fully installed:

 

Setting up a ring and pinion IME is best accomplished by making setup bearings and running a pattern. I've used a variety of tools over the years to try and measure pinion depth, which in theory can give you the right pinion shim the first time, but unless you are using the same gears in the same type of axle over and over and over again you end up spending more time learning how to set up the tool and read it correctly (and possibly STILL not getting the right pinion shim the first time) than you do just using setup bearings and running a pattern. Ultimately, regardless what any tool tells you the pattern trumps it, because the pattern is the true measure of how the gears mesh. I have a buddy that owns an off road shop and has probably setup up in excess of a thousand sets of gears over the years and that's how he does it as well. His advice is to start with the factory pinion shim, even on new gears, and go from there. I've set up probably a dozen sets at this point and that's how I've always done it as well.

Making setup bearings is pretty easy, just get an extra bearing for each bearing where you need to make a setup bearing. On the Super 60 you will need 3 setup bearings (rear pinion bearing and both carrier bearings) because of where Dana/Ford locates the shims. These bearings are press fit, so you need to open up the ID of the bearing, which I have always done with a carbide bur in an electric grinder. It takes maybe 1-2 minutes of grinding per bearing to open up the ID enough to make it a slip fit. You can carefully clamp the bearing in a vice (clamp only the protruding part of the inner race just enough to hold it still), and then run the bur around the ID. I like to count to 30 while I do this, stop, check fit, and repeat as necessary. You don't want to go too far and end up with a sloppy fit. It should be just loose enough to get on and off by hand with no slop. I've heard of and tried, other ways to do this over the years, but this is IME the best and fastest way to do it. I've read about guys using brake cylinder hones or small engine hones. I did that for an hour one time and removed maybe 0.001" of material when you need to remove probably 0.003-0.005" of material. I don't recommend that route. Obviously thoroughly clean the bearing after grinding to remove any metal particles.

To set backlash you need a dial indicator and some type of holding fixture. I use a simple magnetic base fixture and dial indicator I bought at Harbor Freight probably 25 years ago. I had to make a new back plate for the indicator to allow it to be mounted to the fixture, but this setup has worked for every axle I've ever done, as well as for setting endplay on the shafts in a couple dozen transmissions, and cam & crank endplay in a dozen or so engines.

Another thing worth noting is that I do not bother with the pinion spacer to run test patterns. If you simply don't install it, and carefully tighten down the pinion nut (use the old nut for gear setup, then install the new one at final assembly so it only gets used once) until there is no slack, then start checking pinion bearing preload until you get it right; that will be fine for checking the pattern. I use an inch/lb. torque wrench to check the preload. I set it on the lightest setting (17 in/lbs for this axle) and tighten the nut until it just clicks. Then check it at the highest setting (30 in/lbs for this axle) and make sure it spins the pinion without clicking.