I've ran this module in 3.5 about a year ago. It was great, although a bit tough. Now for your questions:
1) We didn't level up during the adventure since it all happens during one night.
2) I used the NPCs to help my players during battles. I think it makes sense for everyone to contribute, since they are all in a dire situtation together.
Just a few thoughts on the modules I've ran or played:
Tomb of the Iron Medusa: An excellent module featuring interesting combats and a rich backstory. Well done!
No Response From Deepmar: Couldn't find anything interesting in this module. Especially the story seemed bland..
Crypt of the Everflame: A tough dungeon-crawl, not ideal for inexperienced players.
Masks of the Living God: A great module not for combat-oriented players. Really enjoyed it!
Fangwood Keep: Played it recently, and had fun with it.
Name: Lorenzo Feodor
Crashed to death by the Aberrant Promethean. Had a chance to run away, but didn't take it...
The party decided to open all three doors leading to a certain black pudding at the same time (aka splitting). The poor fighter failed to close his door when everyone else did, and got devoured by the ooze. They didn't even find his bones...
Alezandaru was the first to descend and was ambushed by 4 ghasts. He failed his second paralyzation saving throw, and two of the ghasts kept biting him until he died.
Name: Father Lucian
Getting bitten by dire rats summoned from the Splatterman (and an empowered magic missile).
Name: Sir Tiberius Kane
Getting hit by 2 maximized magic missiles from the Splatterman.
Well it's not entirely free will.. I strictly forbid evil alignments, and I strongly discourage even neutral ones. I like my players to be heroes! As Pendagast says used to be the norm back then.
Back in the days, when I ran this, I created cards with 3 different checks with different DCs. Each card had an easy, a moderate and a hard DC, with different rewards depending on the check. My players had a blast and still remember the chase as one of the memorable moments in our gaming table.
What dartnet ment, from my point of view, is the idea of running only Shattered Star, but in game at the same time as the other three campaigns.
I would wait to read the entire Shattered Star AP before trying something like that, but for now, I think the intention of ths AP is to revisit old locations, meet old friends etc, so your idea kind of ruins this intention.
As a DM: The group is somewhere in the Storval Plataeu (RotR)
When we played this final fight, the players won with relative ease. The main reason is she cannot do enough damage to present a serious threat. By the time the players reached the final fight, they all had some way to fly (as expected in these levels).
Depends on party composition. If there is a healer (or two??) you should all concentrate on killing the monsters faster. But when no healers exist and surviving becomes more difficult, you should focus on defending and holding out.
Posting only about the APs I've ran as a DM, played as a PC or read:
Shackled City (PC): Flood Season
Every wizard/sorcerer/cleric in my campaigns use read magic to identify the scroll. To be exact, they try reading it with Spellcraft, and use read magic when the check fails.
Magic is written in a different notation and no commoner should be able to read it.
Name of PC: Gerald Arrowswift
Trying to defend Sandpoint against the giants, the dwarven ranger Gerald spotted Teractinus searching the Old Light. He quickly moved in to investigate along with Dienekes, the human fighter. Unfortunately for them the stone giant found the time to bury Gerald under a heap of rocks (favored enemy: dwarves helped a lot).
Considering the Academae, I'm more inclined towards an alternative explanation. Perhaps they were discovered by some high level wizard of the Academae, one who struck a deal with them never to reveal their true existence in exchange for power.
Just food for thought..
After selling everything they had, and calling favors here and there, the PCs managed to cast a raise dead spell on their fallen comrade, the wizard Alinica. The moved once more for Thistletop. This time they didn't fall from the bridge. But when they arrived onto the island, the goblins unleashed an attack on them. In the aftermath of the battle, 3 character's laid down unconscious, and the dwarf ranger tried to heal them. He started with the paladin, then the cleric. When he arrived at Alinica's body, he found her dead...
During the initial investigation of Thistletop, the party tried to cross the bridge disregarding its state. Three PCs fell to the water, but only the wizard Alinica drowned, since she was not healed after the encounter with the druid.
Indeed, favored enemy: humanoid(giant) is a must. I want to make it a prestige class, despite the fact that it is not prestigious - due to the nature of who signs up - because this certain player loves the idea of joining a Golarion-specific prestige class.
I'll just wait and see the outcome of their visit to HM, and give my players the choice to possibly rebuild the Order.