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Sorry for the delay in answering! 

1. At the start of a combat, have everyone roll it, and go from highest to lowest. If the ship is taking actions, it is either in conjunction with the Kobold at the station or, if there is nobody, in conjunction with the Captain's turn. 

2. There is always a minimum of 1 die for a roll; lucky them!

3. Yes, though there are other ways to extinguish a fire, including manual intervention or venting the atmosphere to the vacuum of space.

4. In the event there is no other ship or other target, yes, you can have the attack against the ship simply miss. 

First, for the sake of clarity, the Koboldly Go! file is the most recent version; if it's got the art and not the watermark, it's the revised version. I did not do a great job making that clear, and that's on me. Apologies.

Another aside before we begin, while it's definitely possible to imagine the players as the only Kobolds on the ship, that was not my intent; the players are the Spock, Kirk, and Uhura, but there are still dozens of other kobolds running around working on and maintaining the ship or causing minor havoc. That said, if you want to imagine them as Han and Chewie, go for it.

Now to your questions, in order:
General:

• A complete success on a repair grants the room a bonus die of power for the turn; this is a case of a specific rule overriding a general rule. Depending on the room, that may end up granting it an extra die for what it does but that is incidental.
• The wording is awkward as is slated for a significant revising in the not distant future, but it is intended to function the same way; you have a pool of dice for attacks equal to the power to your weapons minus the power of the targeted ship's engines. You can make any number of attacks with this pool (minimum of one die), concentrating them for more accurate hits or spreading them out to potentially affect more systems. Most notably this is not intended to use the stats of the Kobold operating the weapons systems... they're telling the system what to do but the computer's hardware and software does the actual targeting.
• It is intended to have a planning phase each turn. Sometimes they can be quite short, like "Do what we did last turn, hopefully better this time".

Abilities:

• For Make it So, the bonus expires when a new order is given, though I would permit an old order to still grant its bonus if the receiving kobold was not aware of the new order, provided they're not trying to game the system that way.
• The Communications Officer is intended to be especially good at Planning and Helping, provided their allies can receive their communications. When they get a mixed success on Help or Plan, they will grant 3 bonus dice, and potentially 4 on a complete success. As a sidenote here, I'll be removing strict sensory mechanics going forward so as not to cause issues for people who want to play, for example, deaf or hard of hearing kobolds.
  • Do let me know if you feel like this is a little too strong/overwhelming, I'm considering moving it down to one bonus die.

Combat:

• Yes, NPCs and NPC ships do roll in combat, this is an intended diversion from the Blades in the Dark norm.
• Dodge is meant to be taken as your action on a turn, to defend yourself or another Kobold. That said, it feels a little lackluster, especially given that the number of attacks can easily overwhelm the number of potential dodges, so look for this to change... I haven't decided on precisely what the change will be yet.
• You are absolutely right that this section is terribly confusing; I believe I answered it in the general section above, but do let me know if you're still confused.

Rooms:

• It is intended that the Captain is the one who can re-allocate power. In the event a captain is dead or otherwise incapacitated, it would be good to either elect a new captain quickly or to have a pre-established chain of command; if you want to make it easy on your players, you could have an NPC Kobold be a First Mate who can automatically step up to allocate power in the captain's absence. That said, if there's nobody in the bridge and no power to engines... that's a bad place to be.
• It is intended that one scan reveals one thing, so you could learn the positions of the crew or the layout of the ship (including what room does what), but not both with one unit of power. There is no roll associated with this, it just works. You can get both with 2 units of power (or just remembering the layout from a prior turn).

Thank you for your detailed questions! I hope this helped resolve the confusion.

Good news! I'm actually working on the response right now, and will respond to your original post when I finish.

I wanted to let you know that I’ve seen your questions and hope to have answers for them soon. Thanks for your patience. 

Thank you! And thank you for your kind review. :)

You are correct on both minor issues (Including what caused the second one) and I plan to correct them in a future edition. 

https://coffeesnakestudios.itch.io/koboldly-go

I completely agree with this suggestion. The lack of ability to set prices for these precludes me from making any of these projects. I need to be able to continue to create and to support that creation.