Killing Griff's gang is mandatory, I prefer to keep them around for the shops, and you can save Stingtail too by killing the hitman sent to kill him.
Never really figured out where toget Broken bottle.
I kinda left Fort Joy after learning everything and teaching all my team 4 adrenaline 4 stealth and my archer everything so there was very little reason to keep them alive and just turn them into EXP food because... well, look at the inventory as I'm about to go shop at Zaleskar next.