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I'm glad you think my comments are helpful. I certainly don't want to criticize or come across harsh. It is a wonderful adventure and my recommendations are all "nice-to-haves" to consider in any revision. Here are my thoughts to your follow up questions:

1. I actually hadn't considered this! I'd be inclined to have the hatch swing downward, as well. How big of an impact did this lack of information have on your experience?  The player who was opening the hatch was very interested in whether it swung into or out of the lantern  room. I don't think it would make a big difference whether it swung into or out of the room. I think both directions could give different players different challenges. As a GM, I can get tied up in the adventure creator's intent and wonder about details like this. 
2. I'd have ruled the same. I might change the description to "A set of keys inside the desk drawer opens all the locks in the Lighthouse".  That sounds like a good change. 
3. I'd lean toward them being person sized to give players an alternate means of entry. Thoughts on this? I think person size is a good idea so that characters can climb through. A good example of "Jaquaysing" with windows. 
4. It's just so that players need to invest some time/thought into the horn in order to use it. Using the grease and then having the horn alert the ship is a clever solution, and makes perfect sense to me.
5. The intention would be to have an alternate way of warning the vessel! I ran out of word count for the Lighthouse Exterior (you can see I'd have to cut out something else in order to give is expanded mechanics). How big of an impact do you think this lack of information would have had on your experience if they had found the flare? The signal flare could be an impact without some explanations or mechanics around what it does and how it fits. Adding some explanation on how the the signal flare works would help communicate the intention of being another way to warning the vessel.  I think the technology issue (is it a flare gun or torch or some chemically enhanced signal flare like a modern-day road flare?) could cause a "meta hiccup" in the game play.  In a KNAVE setting the signal flare could be a nice place to add a magic item. Maybe a magical flare gun (with one use) that could warn the approaching vessel, but also be used as a range weapon against Macneil and O'Connell  with the added danger that it could light the ochre pain or lamp oil on fire (yikes!) or blind people too close to the exploding flare. 
6. Since it's made with lantern oil as a base, I think that's a fair assumption! Personally, I'd just have it react the same as lantern oil if players decided to light it on fire. Given the storm, though, I don't see a fire spreading very far.
7. Super useful feedback! How did the fight play out with fewer attacks? How do you think it would have played out with lower AC? The fight was a dangerously close one because the PC was the only one in the Lantern Room when combat started. The other PCs were at the bottom of the stairwell (to keep it from collapsing - they figured that out). Macneil got some lucky rolls and the first PC had some unlucky rolls. Once the second PC arrived, the fight turned quickly in the PC's favor. The first PC had missed hitting Macneil with a KNAVE web spell. But, later shoved Macneil into the sticky web that (I ruled) was on the wall behind Macneil. Once stuck in the web, Macneil was struck down by the PCs. The first PC only had one Knave "slot" remaining for health. 
   1. As far as his weapon, I think any kind of tool around the lighthouse (e.g. an axe, a hammer, a knife, etc.) would be justified. Just a sentence or note on whether Macneil is armed or not would be good for setting the tone and intent of Macneil. Just like if Macneil is wearing any armor. These are good "signposts" for the players to recognize what they are dealing with, as well as any role-playing dialogue the GM provides. Is Macneil standing around in some armor pieces from the city guard who were sent out to investigate the lighthouse? Macneil is on "divine mission" and "watchful" - wearing armor or having some form of weapon in his hand could be good signposting. On a side note, the first PC into the lantern room used the sledge hammer as a weapon to attack MacNeil - trying to surprise MacNeil. I gave the PC first attack for the creative way to use the hammer lying about. 
   2. As for the AC, I pictured it more as a result of his mania/psychosis, i.e. he can take a hit and just shrug it off.  The intent was really just to make him a greater threat. Any overall thoughts on this? It seems like you're leaning towards a reduced difficulty for Alistair.  If a PC (at first level)  faces Alistair alone, the PC is in for a tough fight. I nerfed Alistair's threat because I wanted the time crunch and challenge to signal the ship as the main threat. I didn't want Alistair and O'Connell to be too big of an obstacle. I think the first PC in my play through was unwise to attack Alistair by themselves to begin with. When I run this adventure again, if I keep Alistair a big threat, I will add more physical and behavioral traits in order to signpost the danger/threat from Alistair. Maybe, I will make Alistair bigger, stronger, fierce, or doing something like "holding the sledgehammer with ease in his powerful grip."
8. Do you think this needs more emphasis on page 11, or is this more of a new system (Knave) issue? I don't think this needs more emphasis.The only other system I play with is Advanced Old School Essentials. I think a GM with some experience will be ok with using a search  mechanic that fits with their chosen rules system.  This is an example of where I didn't prepare well enough for running this adventure, but will be much better on the next run through. 
9. Noted!
10. Do you think this needs emphasis somewhere in the adventure? Ben Milton, who created Knave, often says it is important to give the players a lot of information. The imagery and idea of a lighthouse is iconic, but I can imagine some players (especially younger ones) not having a clear sense of how a lighthouse keeps ships safe or how an older light house works. A few sentences on what the lighthouse does and how it works will clearly communicate the importance of finding the wick, oil, and lens.  
11. Another good question I hadn't considered! Do you think the set of keys is enough to cover this, or would you suggest explicitly mentioning Dylan also having a key? It makes sense to me that Dylan would have the keys to the manacles because it is my assumption that Dylan was watching over Malcolm. I would have liked the adventure to explicitly mention Dylan having keys to the manacles - maybe even explicitly describing them as manacle keys in the even the PCs have not encounter Malcom Fraiser or the dugout yet. 

Happy to offer these thoughts. Hope it isn't too much.