I'm a bit late to the party, but I know you were talking about the front and rear dana 44s being different. The front unlocked is an open diff. while the rear unlocked is limited slip. This may have to do with why the covers are different.
But that aside, just read through the build, great work so far. Definitely good to get the maintenance and armor out of the way before building it too much!
I never make the same mistake twice - it's more like three or four times.
Build - http://www.jeepforum.com/forum/f22/unlimicon-build-1477723/