Bolt pattern is going to be the biggest issue when looking for a D44. The only ones that you will find are from a Wrangler equipped with one, such as a Rubicon (which are generally pricey), or an XJ/MJ (which are getting harder to find). The ones from the late 80's/early 90's FSJ Wagoneers are a six lug pattern which means adapters or 2 spare tires.
I would suggest going the route of a Ford Explorer 8.8. They are similar strength to a D44, have the same bolt pattern, and are extremely easy to come by. The later 90's versions (can't recall exact year) are equipped with disc brakes. The only downfalls are that the pinion is slightly offset to one side and they are slightly narrower than the Wrangler axle, neither of which is anything to be worried about. They are probably the most common swapped axle in your application.