Aftermarket glass and/or thicker weight vinyl will all effect stack height. It is very challenging to get even a factory top with thin weight vinyl to clip into the manual top clips. You have to fold it correctly and make sure there is no binding anywhere. With an aftermarket glass top, I would guess there is no way to fix that easily. With a power top its not as noticeable since the rams will hold it down even if the stack height is to large.
In order to have a shot at clipping it, you would have to have the factory 32oz vinyl with the non zipped plastic rear window. Even then you have to stop the top halfway and pull out the mid fold. There should be some posts about that around here.
The only other suggestion I have to to alter the clip location. It is just bolted to the inner qtr. You could make a small extension to the metal end to raise the clip up to where the frame is, to at least get it clipped. Stack height will be too high, but at least it won't fly open while driving.
