Removing front windshield and back glass

You are correct there are square notches should be four on each side that the bows rest in. Now comes the part you don't want to know. The bows have to go in the same order they came out. I am not sure what the difference it but I think its the length and the amount of bow in the rod.

Def put them in the same way you took them out! The roof's line changes as it goes from front to back and each bow is cut and shaped to that line.. Luckily I labeled all mine before I took them out. Also, while I have them out, i coated the entire top in por 15, now going to put some Peel and Seal (cheaper dynamat alternative) on there before installing the liner..