The inner driver side shaft does pull out of the housing/diff. It has the same spline as the passenger side CV stub shaft into the diff AND has the same c-clip on the end of it which usually requires it to be extracted by inserting a yoke (Y shape) pry bar under the flange end and tap it out with a hammer. I pulled mine out of my '02 Tracker again a couple months ago and I had to get serious with the hammer to extract it. I ended up wrapping a rag around the handle of my yoke shaped pry bar to ease the vibration on the hand during hammer impacts. It also sometimes helps to rotate the shaft between blows to help center up the c-clip in the spline groove. Either way, easy or tough, it does come out.
Just to be safe, be sure to count the number of teeth on BOTH ring gears in the diffs to ensure they do match up before the install.