traded my softtop (straight trade on craigslist) for a hard top and i'll list what i remember had to come out and transfered over to make it work
1. top window frame bracket
2. left and right plastic bracket that bolt onto the frame itself
3. left and right slider brackets behind the seats
4. left and right rear corner brackets
5. left and right rear brackets to hold the roll down window
6. bracket bar that went between those last two brackets
7. the top frame itself
8. then the top
when installing in the other guys jeep, he didnt have most of the front window frame holes, so you either use self tapping screws or drill and screw.
remember that if its a yj your door will not fit anymore, this is because your have round doors, of if you have the square doors, the hinges might be off so it wont close right and you might have to give the top hinges a little love tap to make it fit right. the most important part of the whole deal would be your brackets, sliders and frame. everything else can be replaced fairly easily.
this is just want i have found to be true. it will not be the case for all jeeps, so good luck.