A few questions

[capnq]

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How do you change what weapons are used by ministers (for example, if I turn on Ship design minister and I would like to use, for instance, Torpedoes)?

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To change that, you'd have to modify the corresponding < racename or Default >_AI_DesignCreation.txt

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What are your favorite techs 1-5?

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Hard to say; I play a lot of different races for variety. I tend to go heavy on seekers in the early game, so Missle Weapons, Organic Weapons, or Crystalline Weapons tend to get priority.

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Is there a way to stop the ship construction minister from constructing a certain item?

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Mod *DesignCreation.txt and/or Default_AI_Construction_Vehicles.txt

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what tech area do you research to get Atmosphere ConVersion Plants? (Planet Utilization, right?)

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Yes.

Most of the rest of your questions depend entirely on your preferred playing style. One of the great strengths of SE IV is that there's hardly ever one "best" way to do something.