A couple of weeks ago I spent a couple of hours working with
@epoxid over Skype and learned about how he designed the top and where everything was suppose to line up. I cannot thank him enough for his time, I really appreciated it.
Something that made my top slot in much better is if you do the following. Look at the underside of the rear edge of the roof. You will see a raised bevel that goes along the underside, that is suppose to go in the rear gasket groove. Place the roof on the car then use your finger to make sure that the bevel is going to go directly into the gasket. It is easy to have the top get misaligned after you slot one side in. The problem occurs when you get one side in and then the top goes diagonal toward the other side. If you have a second person, it works well to have both people press down at the same time so the top stays in straight.
Playing around with the number of shims did not make a difference for me, however you have to make sure that the shims are lined up and the hole they make is not too close to the edge of the plastic. Otherwise you won't be able to get the latch closed. What changing the number of shims will do is help you create a straight edge along the windshield and let you adjust the gap so you don't chip either the top or the car.
At the front edge the bevel goes on-top of the gasket not behind or in front. Once the back edge is straight, the front seemed to go much easier.