After several days taking apart the Honda Pilot, it turns out that the compression test and leak down tests that were done on the engine earlier this Spring were 100% accurate. Although not apparent at first, once the valves were removed from cylinder 6 it was obvious that the valves on the intake side were indeed very bent. After picking up some new valves at a local shop I did a valve lap job and then completed the reassembly of the cylinder head.
I am still a long way from trying to start the engine back up, but at least everything that I am doing now is putting things back together.
Definitely a pretty big DIY project, and one that I would not want to take on if I needed to use this vehicle in the next few days.
Cheers