You say it has had side windows put in If these are after 'market windows' are they the exact size and shape as genuine, also have they been fitted in the correct position?
I had a hardtop with after market windows fitted along with genuine trim panels, BUT the windows were longer than the hole in trim panel and the corner radius was different. Took the trim panels out because they never looked just right.
I can take measurements of the trim panel window aperture if this helps.
Stuart