Is the top installed and now not lining up when you try to close it?
Or, is the top not lining up with the frame AS you are trying to install it?
If that is the case. Take some measurements from the top and assess whether it is the top that is crooked or your framework. If the top is crooked, take pictures of the measurements you've found to be crooked and send them back to the company you bought the top from for assessment. If the top is off, most manufacturers will gladly replace it.
However, if the frame is off - that might be something you have to fix before you can finish the install. Something to think about is maybe your old top was help holding your frame in place and once it was removed, your framework fell into more of a crooked state than it was previously.
Either way, g'luck with the install!