That is the same coop I started with. Your additional security measures are pretty good, however, I can envision how a raccoon could stand on the roof, lift the lid enough to reach in and grab a bird, and let go of the roof, with the bungee cord staying in place, and snapping the roof shut again. I think putting a couple of screws in to keep the roof permanently shut is safer. I never found a reason to open my roof in the 2 years that I used my coop. Also, a raccoon can open the poop tray and grab a bird by the legs and pull it out. I don't think that is what happened, because the tray would have been open and you would have seen that, but just so you know, a safety hasp and lock like you have on the doors would be smart. If you haven't done so already, I would secure the hardware cloth with screws and fender washers also, those tiny staples they use are not going to stop a raccoon, and once it gets into the run, the pop door would be easy to push aside.
Unrelated to the predation, you don't really want to close the vents, there is not enough ventilation with them closed. I never closed my vents, and it is not a problem.
