Dual top models come with the frame attached and folded down with the hard top on. (you are supposed to take the top off and the softtop out). The windows and door surrounds were in boxes. I guess you did not get those.
The surrounds cost about 100 used. Yes you can buy LJ windows but they are expensive. You probably are missing the tailgate bar also, and I don't know if the tailgate bar clips are attached to the tub.
2003 TJ, 33" BFG AT, 2" BL, 2" BDS spring lift, Truck Lite headlights, Homemade sunrider top.