Yikes, I could go into the whole procedure, but you're much better off buying the Helms Manual. Getting the shafts lined up, and the cover back on just takes some fumbling.

-edit-
Ok, so I thought better of it. If you changed out your differential, you absolutely should get the roller ball bearings instead of the tapered roller bearings that probably come with it. Make sure that your reverse idler gear is installed right side up. If its not, you won't be able to shift the gears, although the housing will go on. Make sure you have all of the shafts lined up right and in their housing. Ensure that you have your shift forks lined up with the shifting assembly. You might have to take a piece of safety wire and hook it around the little shifter shaft to keep it upright. The housing will go right on, with some easy taps with a rubber mallet. Don't tap too hard though, and stop once you feel resistance.