Hey! I know you asked a while ago, but hopefully it can still help.
I've been running for a few months, party is up to generation 4 and have reached the Kelp Forest. I'd say in general the answer here is going to be "depends on how the referee wants to run it." I think that's you here, but not sure. Here's what I would do:
1. Yes, definitely starts with ammo. You could do one slot's worth or you could maybe do as many slots as they want to fill. This hasn't come up for me a lot because the player's have generally used melee weapons. I also forgot there was ammo! Harpoonbow seems especially tricky though since it doesn't seem like there is a way to replenish the ammo. I'd probably just let them have a slot and count it as enough, but honestly hasn't come up a ton.
2. I don't let benefits like that accrue generation to generation. I like the choice between doing damage early on or identifying something, it makes them think about time and need to decide between risk now / reward later.
3. The way I read it, no. Forage and explore seem like they would take everyone working together. It also will make it way easier if you allow them to "split" a turn like that because they will be able to do much more than they would otherwise. I always viewed the turn choices as everyone needing to do them together.