I worked on trying to solve this for a few hours today and read up on forums for a few more. No matter what I did to sync up the transmissions, the clamshell support arms became uneven at some point in the operation. The driver's side has a lot of tension on it and starts to dig into the weather stripping as in the photos. I made a youtube video that captures my issue and bewilderment.
https://www.youtube.com/watch?v=_rPTbLx6-sM
I'm not sure where to go from here.