Couple of things, first of all any Jeep optioned with the "off road" package got the D44 rear. This includes some (I would venture to say "most" Sport models (of which the Sahara (and Golden Eagle) was a special edition), and I believe even the "X" models had the option although it was less common. If you can find one of these rear axles, obviously they would essentially just bolt in. Rubicon rear D44's are relatively easy to fit but they're slightly more complicated in that they come with an air locker from the factory (non-Rubicon Jeep D44's do not). Note that a Rubicon D44 will be geared to 4.10 while non-Rubicon D44's could be anything from 3.73 up depending on transmission and other options, so you may or may not need a new ring and pinion depending on what your wheel/tire combination is. As for the fronts, the TJ Rubicon D44 front isn't any more difficult to swap in than the TJ Rubicon D44 rear (i.e. it has an air locker so it's slightly more complicated than a straight bolt in).
Now, as was mentioned previously, the supply of 'new' TJ D44 axles is drying up. You still shouldn't have much trouble finding at least a rear in just about any junkyard if you want to go that route. I just want you to know that you can fit JK D44 axles underneath your TJ, just to give you another option. Of course they are wider than the TJ axles, so they require some fabrication, but I've seen it done before.
One last thing - unless I'm mistaken you can put disc brakes on a D35.