1. Sometimes when opening the GSX menu, I get the loading please wait message indefinitely and it never displays me any options.
As explained in so many threads about this, if this happens, you need to check if the Couatl engine is still running, because it might have crashed, possibly due to problems with the Navdata API or Simconnect stop responding due to having too many objects in a scene. Just start it again from its icon on the Desktop.
2. The Simbrief banner continues to display red despite clicking the reload Simbrief button. Opening and closing the menu seems to resolve this and it becomes green again.
The Simbrief button doesn't auto-refresh if a connection is made successfully while the menu is optn, but it will surely refresh if you click it again.
3. With the PMDG 737-800, when locking gear for pushback the ground agent is clipping inside of the nose gear. Is this just a byproduct of the lower nose gear rather than say the A320?
Of course. That's not really a "bug", more a need or a new animation for smaller airplanes.