After discovering that there was an alignment issue with our sunroof mechanism, we decided to completely remove the roof to troubleshoot the problem. We didn't necessarily have to remove the liner but we were curious what it looked like under the padding.
As the liner was reinstalled, we noticed a broken piece at the corner of the roof.
This little black plastic piece (called a sunroof stop) was the reason why our sunroof wouldn't close. Because it was cracked, the roof wouldn't align itself after it was opened all the way.
You can't find these through Honda any longer so luckily, we were able to buy an aftermarket replacement. The purchase actually set us back $50 so we decided that for our next project, we'd rather just make our own =).
We'll see if this fixes the issue. Stay tuned!