Hi! Thanks for asking for clarification.
The way the showdown roll is intended to work in Bump in the Dark is that:
1. You get 1d per question that you are able to answer using at least one unique clue
2. A clue only counts as answering a question if you haven't already used it to answer a previous question
I can see why the way it's written is somewhat confusing, since "each clue used only contributes to your dice pool once" could be read as each clue contributes a d6 to the pool, however, this is not the intention. I can look at clarifying that passage.
I will say that the showdown roll is the last bit I still find myself tinkering with. Overall, I think it works well this way: you technically only need to find three clues to be able to get the maximum dice (unless you have the "diligent" pact ability, which awards you for finding all the clues before the countdown clock fills), but in practice the more clues you find, the easier it is to come up with a theory that makes sense fictionally. I've only once had players insistent on rolling with only three clues (experienced Brindlewood Bay players, interestingly); every other time they've wanted more to be able to feel like they could come up with a theory that makes at least some sense. (I'm also pretty generous with clues when I'm running the game, so it's likely they're going to find more than just three anyway -- but if they can't figure out how to answer the second question with the clues they have, it's still helpful to have more clues).
In early drafts of the game, the showdown roll worked just as the theory roll does in ECB, where if you answer a question with multiple clues, you get multiple dice for that question. In practice, I found that players were getting a shit ton of dice (usually 6-8) for the showdown roll in a way that felt really uninteresting to us at the table. One solution for this is to push the countdown harder, so that they can't find so many clues in the first place before having to deal with the monster, but we tried limiting it to only 3 dice maximum (4 with the pact ability) and it worked really well at the table.
I have played around with making it more like The Between or Apocalypse Keys, where there is a complexity rating equal to the countdown clock but that hasn't felt quite right, either.
I did draft this version at one point, trying to mechanize the race between finding clues and the clock filling. I may still playtest this version, and would certainly be open to feedback on it:
Take 1d for each unique clue you use to answer one of the showdown questions. Clues can be used to answer multiple questions, but each clue used only contributes to your dice pool once. Then, take -1d for each filled segment of the countdown clock. If you are left with zero or fewer dice, roll 2d and take the lower.
Regardless, I appreciate your feedback and would encourage you to try what makes sense to you, and report back if you're willing! I think it works well as written (or as intended, if the wording is confusing) but clearly I've never been 100% firm on that, or I wouldn't still be tinkering with it long after the rest of the game is done.