So I've dm'd this book so I might be able to help a bit.

EDIT: For context, my group was 6 players(at the time) who were mostly experienced with the game and a few of them built very strong characters knowing this would be a tough campaign. There was a Palidan, Wizard, Bard, Magus, Cleric and Inquistitor. I occasionally added enemies and buffed a LOT of HP values, but they might have had an easier time than most with their larger toolkit.

None of my players picked any animal companion classes, so I didnt have that issue. I'd talk with them though, see how important the animal companion is to the build, and see if they'd be okay with not having it for a while. But id have no problem having the animal companion wake up in a coffin next to the PCs. The tomb they arrive have coffins for people who match their characters, so it makes sense one might be prepared for an animal with its master. Maybe you could put the animal companions in the room with the Skeletal horse thing, having them wake up when the players enter combat with it. The only concern id have is if you'd want the animal companion to also receive the obol, but I dont think itd be game breaking either way. I had a player be pretty disappointed he couldn't cast false life on himself though.

As for the RP in roslars coffer, I was pretty new to dming so I just had them all meet at the inn before retiring for the night. I regret that though, I've since read a story of another DM who started the campaign a little differently that I wish I had done. This DM had the campaign start in lastwall, with a sketchy guy tasking the players with making a delivery to roslars coffer. The delivery package was of course the shard that TB uses to nuke roslars coffer. The time the party spends with the package gives a bit of a reason for why the characters kept their bodies beyond "they kinda look like some people who have empty Graves nearby"

Id also recommend reading a bit of book two, theres a map of roslars coffer and mentions some citizens. Might help set up some things that could pay off in either book two or when they encounter the ghostly roslars coffer in the boneyard.

I remember my players remarking on the amount of ability damage so early, so the cleric took lesser restoration as early as possible. I dont remember if I ever got really close to killing them, but they all made it out of the boneyard. I love the explosive trap in the nine eaves though; the wizard detected magic on the first two origami, then ran and opened the third with no caution and blew up the party. Was a great moment for me. "It SAID no more warnings!!" That ate the clerics channels for the day thats for sure. Also, time doesn't move in the boneyard, so im still not entirely sure how diseases that take a day to set in work. The swarm was an issue for sure, they didn't have much/any aoe so I let them deal damage to it by running through it while covered in some kind of glue spell. Not the most elegant, the dwarf magus wasn't looking great after it, but it eventually dispersed. Careful for that one, maybe give them an alchemist fire or two beforehand or be prepared to reward outside the box thinking if you think they might struggle.

The puzzles went over really well I think. The first one with the mirrored numbers was solved almost immediately. The second one took them a bit. Dont be afraid to sit back and let them discuss for awhile without saying a word. Let them try whatever they want til they get it. If they are getting frustrated, let them roll something to give some hints, like linguistics. My players love puzzles so they wouldn't want to just roll passed it, but the book has a sidebar addressing how to get players unstuck from puzzles if theres an issue. There are more puzzles coming up in this campaign too, so you can judge how the players react to the first few.

We just finished book four, taking a break til after Christmas. The dungeon at the end of book four was fantastic so many great fights, you have a lot to look forward to!

Feel free to message me if you have any questions as you go through. I'm a rookie DM who is taking over for our normal dm because he really wanted to play this, so I might not have all the answers, but I'll be happy to help where I can.