If you bought the hardtop used, it can take a while to, "settle," to your car. It took my top about two weeks. I would recommend having someone push both forward and down on the top, as you tighten the bolts, every few days for a while. That is what I did and my top now fits very well.
If could be more specific as to how large the gaps are and on which side they are on, we might be able to help you out more.
