Thanks for taking the time to do that, @Brandon_R, and for posting these photos. I’m glad to hear you’re up and printing!
Regarding the lid closing flush with the top of the Glowforge, @johnse is correct. That’s a variation that we’ve been seeing on these first machines - It doesn’t normally impact operation in any way.
Each Glowforge unit is tested on a flat granite slab, so making sure the surface under your Glowforge is flat assists with the lid closing easily. As others have mentioned, you can try inserting a shim or spacer under the center of the printer. If that doesn’t help, try moving the shim to either edge. It may require some experimentation to get it leveled so that it closes properly.
Would you let us know if these suggestions address the issue you’re seeing?