Hi,
1) the move states:
Your animal companion is trained to fight humanoids. Choose as many additional trainings as its cunning.
Then -
When you work with your animal companion on something it’s trained in…
and you do something as indicated in the list, you add bonuses as written.
SO: the ranger descrives his move (as always), stating how he works with his companion, then he rolls (or takes damage) adding the relevant bonus.
Scouting the dungeon may be Defy Danger or Track, but the ranger must partecipate. HAving the druid to translate is so funny!! I wouldn't even require a roll.
2) you subrtact the ARMOR value from the damage you take. A hit having the "Piercing X" tag, counts armor as X points lower. You don't permanently make armor less effective. You treat it as X lower for THAT hit. A shield gives its bonus, period. BUT, if it'd be fictionally impossible or illogical, you could discard the bonus. The GM doesn'r rule this out. The fiction does.
3) Combat should take any amount of time as not to be boring, or useless. There's no fixed amount of time. Keep in mind that if it's your first game, you take a bit to get used. It's quite common.
As for Defy Danger, THE PLAYER describes what he does, then, if it triggers a move, that's it.
Player: "I move fast through blows, dodgind like wind, to do[...]"
GM: "Ok, sounds like a DEX Defy Danger."
4) If the damage come from a hard move, there'sno usually means to avoid it. If It's a soft move, AND the defending player CAN act, he can choose to intervene in the conversation, saying "I step in between and raise my weapon!". That would be good for me.
5) GM" The enemy shoot at you, arrows coming as rain; WHAT DO YOU DO?".
Say, the players state that they scramble somewhere, it could be a Defy Danger. If they roll a 7-9, the GM OFFERS a series of bad things, as per the rule. The enemy being closer is a valid option.
Players roll WHEN they trigger a move. If the move says they take damage, that's it.
The GM is not committed to play step by step. If someone fails, you say the enemy hits you. Take damage. Or, the enemy misses, but it's closer, now it'has a clearer shot.
And always: "Wat do you do?"
Remember, DON'T call for rolls. THE MOVES trigger the rolls, not the GM.