Let me get this part out of the way; My rearend was leaking.

I figured it would be an easy job to pull the pumpkin off and replace the gasket. Being a novice wrencher, I had no idea how involved this would be. Long story short, I have a new gasket installed and the pumpkin bolted back up.
However, when I try to re-install the axles, it doesn't seem like they seat all the way in the rear-end. The bearings go in and I can tighten down the drums to the axle, but when I turn the axle by hand the pinion doesn't always spin with it.

How do I make sure the axles are installed all the way? (It's a 9" without limited slip)

 

I assume that you've already tried turning the yoke while holding the other axle stationary (or vice versa) to get the splines lined up?

 

Doh! Turns out they were seated properly, I just needed to tighten the bolts down all the way. Truck is moving again!
I ran into another problem though, more leaking...This time, around the pinion seal. It could be that it was always coming from here and I just assumed it was the other seal on the pumpkin. In any case, it's leaking a lot worse than it was.

Without pulling off the axle, whats the easiest way to change the pinion seal?

1. Remove driveshaft
2. Remove Yoke
3. Remove the 5 bolts that hold on the pinion
4. ??? (Can I pull out the pinion with those 5 bolts removed, or do I need to pull the axles again?)
5. Replace with? I'm not sure but it seems like I'm missing a seal between the Yoke and the bearing, there is a gap in between them and when I had it off I attempted to "clean" it and remember removing what looked like thin strings of rubber or pieces of what used to be some sort of seal.

 

Judging from this picture, it seems I'm missing either the Slinger, Seal or Deflector.

 

Axle's are not my forte.

However, I'm pretty sure that if you remove the pinion, you had better know what you are doing 'cause the gear backlash should be checked and set up properly. I'd hate to see you ruin your gears.

Might be time to consult with an axle shop.

 

It's been a while since I set one up, but the Ford 9" rear axle is unique in its design, in that the whole pinion with its bearings and part of the housing comes out the front. It's actually one of the easier axles to repair and adjust. That's one of the reasons why they're so popular in race cars.

Basically, you remove the driveshaft, drain the oil, and take out those 5 bolts. Pull the whole pinion assembly out and take it over to the bench. You don't have to touch the differential or the axles. Be careful, because there's a metal shim ("shim" in the drawing) that goes under the flange with the 5 bolts. That shim is an important part of the setup, and must be put back in. That's what sets the Pinion Depth, which is part of the whole gear engagement/backlash setup. Those shims come in different thicknesses which are selected to adjust the depth that the pinion engages with the ring gear. If you change out the pinion bearings or the pinion, then the pinion depth needs to be measured and adjusted by swapping shims. If you're not changing bearings, leave the shim alone. Clean it and put it back in.

Over on the bench, you can pull off the yoke nut, the yoke, and pull the pinion out the back of the housing. Then you can replace the seal and slinger. You can put it all back together and not affect the engagement/backlash as long as:
1.) You put the same pinion bearings and spacer back in.
2.) You properly torque the yoke nut.
3.) You reinstall the same shim under the mounting flange, and
4.) You properly torque the 5 flange bolts.

Yeah, ideally you should recheck the engagement/backlash any time you have the rear axle apart. But with the Ford 9", you can do the pinion seal replacement without all that.