In the pic of the hard top hitting the roll bar. The flange that has the bolt hole in it (white) needs to go in front of the flange at the end of the roll bar. Then the hard top will fit down all the way onto the top of the windshield frame.
If its too short to make it that far, there are adjustment bolts on the back of those side bars, about 3 inches forward of the main roll bar. Loosen those on both sides as well as the bolts on the bottom of the windshield frame at the dash, then you can adjust the frame to fit the hard top.