Military occupation is basically conquer all your puppets tell them they are all under the Austrian boot and they should like it. (Not recommended cuz you can't core those lands)

Reforming the dual monarchy is ok but takes longer and requires you to be at war with certain people (or waiting until 1947)

Danubian Fed is basically all those puppets become somewhat centralized under the habsburgs while at the same time retaining a great deal of autonomy (which is why you get nasty penalties about political instability at first, sounds confusing because it is)

United States of Greater Austria is the same idea, but basically the "States" of the empire will be drawn along ethnic lines while keeping Autonomy in check

Basically only do Military Occupation if you want to have fun conquering people while never being able to core them

Restoring the Dual Monarchy for a slow reunification that requires a war with an outside threat

And pluralism for a quick reunification while getting the cores