I think you are on the right track - acquire or create what ever aids you deem necessary to help you. You can always discard methods that don't work.
From my table:
Available NPCs that the players don't think will die from a single arrow are likely to be brought along on what they believe will be a big fight. Early on the extra numbers really help stack the odds in favor of PC survival. I've certainly seen them bring along as many NPCs as they can muster - and then summon critters in on top of that.
In this AP getting the "goodies" from those NPCs in the first chapter is a big bonus throughout the entire campaign.
Generally speaking, I suggest having each player "handle" one NPC each (if they have that many) to reduce your workload. If you have a group of more than 5 players, definitely see if one will agree to be assistant GM for you. That player can track initiative for you. Having another player act as "book keeper" later on will be a big help too.
You may want to consider not awarding XP at all, just decide where in the adventure you want the PCs to level and let them know. There is a good suggestion to where to do so in the first few pages of each installment of the AP. This removes a lot of the preasure on you, as you can throw a few more encounters at them, to get them to the loot level that you want them to be at, without having to worry about what that is doing to their XP total.
My players will be sharing loot with the NPCs. The NPCs are integral to the story, work with the PCs to explore and survive their time on the island, so they get a fair share. My group considers it a bit of metagaming when the PCs keep all the loot, simply because they are PCs and not NPCs.
I have delgated the initiative tracking to the players, where one keeps track of who is up next, let's people know when they are on deck, when spells expire, etc..
As for who goes exploring, in my current game, it depends on who is sick and/or hurt. So far, there has been a mixture of PCs and NPCs doing the exploring (Ishirou seems to be immune to diseases -or the dice gods like him :)).
I roleplay the NPCs, but the players control them in combat when their PC is sidelined.
Oh, once the adventure started, I let the players know that if their character died, they would be taking over one of the NPCs until they made it off the island. If they liked the NPC, it would become theirs, and if they didn't they could make a new character at that time. I explained that I found that it broke story immersion if ships kept being wrecked/sunk with only a single survivor (replacement PC). The players all accepted and kinda like the idea.
Heres my experience in DMing this campaign:
GENERAL
* Post it notes are gold. Great for scribbling notes on and sticking on the NPC's page.
* Consider starting it on the ship. Maybe have an encounter or something and then allow for interaction as the PCs settle down for the evening meal. I didn't do this, but wish I had of.
* I added in an adventuring group on board the ship and had them go missing as well. I plan to have the PCs come across their bodies in the jungle and maybe have 1 or 2 as prisoners of the cannibals. I used the PCs in the back of the book as the adventuring group. So far they've served as a bit of red herring with the group associating them with our dear scholar.
* I'd be reluctant to force an NPC on a player after character death like Mistwalker, but I can see the reasoning. If you're having a high kill rate then you probably need to do that to keep a bit of reality in the game. I had my guys create two character concepts with one being their starting character and the other as a back up. The back up would start as an NPC passenger on the ship and would not be found on the beach with the rest of the PCs and NPCs. Theoritically they're somewhere on the island, but are assumed to be dead. Naturally if not needed they're dead, but if needed they'll pop up somewhere.
NPCs
* Based on what I read in the forums I got the impression that the NPC-player interaction could be problematic. I dropped the DCs for NPC attitudes down and made them more willing to help out and share a bit of their past/story. Kept their basic character elements and traits though. I also got the PCs to sort out their watch and then got them to ask the NPCs to join them. It got the PCs to interact with them and some even forged a bond. I'd recommend this.
* Make the NPCs useful to the PCs. When the PCs come back to camp have them heal and treat any wounds, provide food and clean water. I'd also have those in the hunter role randomly find things in the jungle that could be of use to the PCs or the camp site.
* Due to outside factors we've been limited to just three PCs for the last two sessions so Ishirou has kicked around with the group. He's taken an equal slice of loot and xp. Risked life and limb like the PCs so gets a slice of the reward. I plan to keep the NPCs on pace with the PCs in regards to leveling.
* I'd recommend adjusting the NPC skills a touch by giving each NPC one craft skill that might help out. My guys wanted to create makeshift shields and ammunition, and identify alchemical items, but no one had the relevant craft skills. None of the NPCs had the craft skill which was a shame as it would have been a great opportunity for them to contribute to the PCs without having to run around with them. So I'd look at giving 1 rank in the different craft skills to each of the NPCs. Might make the PCs see the NPCs as contributors rather than just dead weight. Craft alchemy could be good to have them mix up a herbal concoction to help saves vs disease which can be real tough for low level NPCs who don't have much of a Fort save.
DREAMS
* Were a bit of a hit and I used the two additional dreams put up in these forums. I even re-used the same dream on different players which was okay because we only play every 2-3 weeks so they'd largely forgotten about it and it gave an opportunity to refresh that information.
MAPS
* in the Souls for Smugglers Shiv thread someone has put up a blank outline of the island. I gave it to the PCS as the map of the island and the guys have been free to mark on it as they like. I think there are a lot of good ideas and downloadable resources that people have put in that thread that are worth getting.
SHIPWRECKS
* I started adding in mundane equipment on board which the guys really liked. Throwing in things like block and tackle, pitons, alchemical items, etc. that the PCs could take back to camp was really embraced. It added to the survival element and creative thinking.
* I'd look at adding in ammunition and possibly ranged weapons here.
* My guys really took to scavaging from the shipwrecks and I got a bit sick of undead and changed it up a bit. I had a thread on it and got a number of good ideas from people that were a bit of a hit with my players.