Is it from Bestop? I seem to recall that mine didn't fit right either, and so I cut it down to size on the straight section, ensuring that the bends on the two channel ends still fit correctly. I don't remember how it came, but at this point I have two pieces that fit the ends correctly, and there's a small gap at the center of the windshield.
1976 FJ40 - green and mostly stock
1996 FZJ80 - not so stock