We had to replace our rear differential on our manual 2001 Forester. My husband had to remove rear axle to take out a part that a seal had to be replaced in. Just trust me, he had to take axle out to do this. Put differential issues right and went to put axle back together but it won't fit back flush on driver's side. Not sure why it won't return to fitting back togther. Finding a differential for a stick shift Subaru took forever. Now thought we were in home stretch and this happening. Any help greatly appreciated.

There is a snap ring on the end of the axle shaft that goes into the Rear Diff.  It has to get popped in. 

 

If the lateral links are removed, a good jolt on the rear brake will pop the snap ring in. 

If the links are hooked up, put a wood block up against the inner CV Joint boot and give it a good hit.  I don't like this option as you can damage the boot.