This weekend I decided to tackle the headroom issue in the runner.
I found a non sunroof headliner and the center dome lights and overhead console. Fully removed the original headliner and the sunroof track and the glass itself.
From there I worked on a way to secure the glass without being able to somehow suction out and disappear on the highway. I came up with aluminum spacers and running bolts through it. It held great and I was able to drill the holes into the side support to make the sunroof be the proper height. Before I brought the sunroof in one final time I taped it off and painted the inside of the glass black so it wouldn't bake the back of the headliner and eventually wear it down.
Once secured I sealed top and bottom with silicone and made sure there was no chance of leaking. Once that was cured I placed the headliner and re attached the handles and visors.
Overall I gained 3-4" of much needed headroom and I never used the sunroof anyway.
After I let it fully cure overnight I tested it by washing. No leaks.