First, the lack of clues in the upper stories of the house. I feel like more can be done here to alert the party that there's more going on than meets the eye. In room 14, for example, a dust trail leads to a window, and there are scuff marks on the sill suggesting that "something" has been placed there recently. Why not go all-out and put the bull's-eye lantern there, so the party at least has a reasonable chance of realizing that some sort of signalling is taking place?
Second, and more importantly, the character of Ned Shakeshaft -- he and his merchant benefactor want to scare off the party and prevent them from discovering the "secret" of the haunted house. So what do they do? They bind and gag Ned and leave him upstairs for the party to find; once rescued, Ned sows dissent, causes accidents, and otherwise makes trouble for the party.
Unfortunately, this doesn't make much sense to me. If Ned wants to preserve the house's secret, then he would be better off warning the smugglers that the adventurers are coming. Then they could set up an ambush or prepare some "ghostly effects" to better scare off the party.
Then there's Ned's story about being knocked unconscious by "unseen attackers..." It doesn't make sense. Ghosts don't bind and gag people. They don't carry them upstairs and leave them for dead. Anyone who hears this story is going to think "Something fishy's going on here. We'd better investigate," which is exactly what Ned and his merchant benefactor don't want.
As I said, none of this makes sense. So what's the best solution? I see a few possibilities:
(1) Remove Ned from the adventure. His plan makes no sense. In which case, I need a new encounter for his location.
(2) Keep Ned, but have him approach the party in town and ask to join them there (either as an adventurer or as a guide). Now he can fill his role as a mole and "cause trouble" for the party without feeding them an obvious lie. My only issue with this solution is that I don't like putting moles in a party, as it's a classic antagonistic-DM move, which only discourages players from trusting NPCs in the future.
(3) Keep Ned, but make him a good guy. He is exactly what he claims to be: an innocent traveler who was attacked and left for dead. But what reason would the smugglers have for capturing (and not killing) him?
Thanks!
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