Maybe you're trying to adjust the wrong parts. My top didn't align perfectly with the windshield when I bought it, but everything else looked right. I disconnected one of the drive cables from drive motor or transmission (not sure what it's called) and turned one of them manually until it looked even.
I opened the roof to the 'service position' and then took a measuring tape from the edge of the roof to the edge of the windshield on both sides, and turn the cable manually until they were even. And Viola! It now aligns perfectly every time I close it.
This video will help identify which cables I'm talking about.
https://www.youtube.com/watch?v=x5AuGmAu7wI
Hybrid Mode
