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There seems to be a bug with the Tier 2 Science Ship.
When I bought it, I can't assign any of my crew members on the Bridge, but I can assign them elsewhere though (Tactical, Culture, etc.). However, I bought the Tier 2 Generalist and it works just fine. Haven't checked if this bug also happens on the Tier 2 Attack Ship.

Sorry I couldn't provide a screenshot, I only have one save file.  I'll try to afford it and take the screenshot then.
EDIT: There's also another bug where crew assignments can't be worked on and it keeps increasing everytime I click on it. Link:
https://imgur.com/a/VN3Ps8T

Yeah man, after the whole thing that happened I was immediately reminded of this game's plot lol.

You can purchase grenades from the same guy you met at the start. He's in a cave somewhere. For spoiler purposes, I won't tell you where, sorry.

Unless you've already found it, of course. There's also a little bit of backtracking. That is, you might wanna revisit some places after you've acquired certain items. 

Yeah, you can enjoy the extended versions of the h-scenes by pressing the down arrow.

No, scope is not required. You just go push those pillars to the side, and keep aiming until your crosshair turns red, then shoot. Done that, and a bridge should spawn which allows you to reach that lever.

For the green hood, you must give a certain item to a Harpy staying on the Isles. You should have all three of those items.