...Wow, I need to rack my brain to remember all of what happened. I think I'll break this down into sections, with the only things I can think of right now.
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OOC Behavior
I honestly cannot imagine how you kept up with all this and stayed sane. For that I give you major props. In my time on CotH, I don't recall an event so big.
However, you did have a deal of trouble with communication. I'd probably be ten times worse. Before it started, an aspect was setup where two guilds would be at war with each other, instead of working to end the madness. I was a leader of one of these guilds, part of a trio. My opinion, I felt, was forgotten when I took a much needed break. I came back, and it felt like my character was made lesser than the others, after all the work I put in beforehand. That my opinion was lesser because of the break--or, so I understood. I would have appreciated an update beforehand, and when I got back.
Perhaps my lack of voice was due to my shutting down from burn out and not talking to others as well. Which I would understand, people not wanting to talk to me.
Disease
Again, I can't imagine how long you thought on this. I'm sure it was as close to perfect as you could make it.
Maybe this is more feedback for the players, but it seemed like people took the concept and ran with it like they were role playing
28 Days Later. As well, its qualities were very quickly discovered and countered. I am unsure how that would have been prevented, or if anything constituted meta-gaming.
Perhaps further clarification and a more solid watch and enforcement on how the disease worked would have prevented this--if such actions were at all possible for the team.
Progression
To me, it felt like little active, fluid progress could be made. Perhaps it was because the town was so OOCly small, but no matter how many times players put the fires out, they kept burning through the whole event. Only once was there aid in the removal of corpses. I understand the want for the area to appear like a warzone, but frustration arises when a player cannot see they had an affect on their environment.
I also understand wanting to keep a story scheduled, spoilers held off, but players will wander and discover things you don't want to. I remember legitimately discovering the boat just off the coast with a team, and then being told that it had to be retconned.
Boss Fights
The only problem I had with these were the length: going on too long. Other than that, they were quite fun. Perhaps a tad schizophrenic and random, but I understand the want to keep us entertained and distracted from foiling your plots.
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That about does it! All in all a worthy, creative effort despite its hiccups. A shame it didn't last longer, but the exhaustion is understandable.