If I understand correctly, the PCs need to destroy/stop the Tree in one foray, since it is said that they shouldn't stop to sleep/recover. Even as written with some fairly weak adversaries, that is a lot of taxing encounters. I'm not sure my group can handle the big fights after so many battles.
Did you have run it by the book ? Were your groups succesful ? Or did you allow more time for the PCs to rest before completing the adventure ?
I ran my group with usually two to three adventures between each AP module. This really cut down on any railroadiness of the original AP. As such, the PCs had a lot more wealth than average for their level and I allowed them a good deal of down-time between adventures.
I had warned them, when we started the campaign, that there would come a time when a timer would start and they wouldn't have any such down-time. As we finished Lords of Oblivion I told the group, this will be your last significant period of down-time, even resting will be difficult.
That made them sit up straight.
We ran Foundation of Flame and then Jenya hit them with Thirteen Cages. While I didn't say they couldn't rest, per se, Jenya 'made a suggestion that shouldn't be ignored.' They opted not to rest and went on to Thirteen Cages.
And this is how I modified Thirteen Cages:
If the group misses the secret door where Gau lives (very likely), don't have her go to Area 5 to stage an ambush. Have her alert the entire complex. The Cagewrights have been working for years to subvert Cauldron to bring about a plan set in motion by the demodands some 500 years ago. They are arrogant, yes, but not stupid. They know this group has been undermining their plans for months, raided the cathedral of Wee Jas, took out Rhiavadi and her guests at her party, and stormed Oblivion. The Cagewrights know this group isn't to be trifled with. That said, they're not going to just wait, room by room trying to take them out one at a time.
Remember that Gau has a move of 40', which is probably faster than the average group speed. The group will get slowed for a few rounds by the farastus in rooms 4 & 5, so Gau will have plenty of time to alert the complex. ALL of the Cagewrights should be at the Tree of Shackled Souls, except for the paranoid one, he's paranoid after all. Ti'irok should gather all of his Flamewarders (16 iirc) and await the party in room 10. If the party doesn't arrive in 5-10 minutes, then he should fall back to the Tree. A kelubar in 7 should get the vrocks in 6 and head to 16 to spring upon the group from behind the stone curtain (also falling back to the Tree if it seems the group has gone the other way). There should be plenty of evidence of recent occupation (i.e. a knocked over cup that's still dripping) so the party knows that they've been detected and the complex is on alert.
I know this makes 13 Cages MUCH harder. A total meat-grinder, but it's a lot more tense. Players who've played as long as yours should recognize that its time to call in Nidrama, the hound archon from Test of the Smoking Eye, Saureya (if feasible), and any other big guns they can.
* I allowed them to level immediately.
* All healing spells, wands, potions, etc. were blessed by St. Cuthbert and were empowered and maximized. I would ask for random things at first to cover this; "What's your CHA score?" "Make a Heal check." "I need a WIL save." That sort of thing. After about the fifth time, the cleric stopped to cast divination. St. Cuthbert said something like, "You tread the righteous path; the dangerous path. So, yea, I pad the soles of your shoes as you walk it." Players thought it was cool. It made combats liveable, but by no means a cake-walk.
Sad I'm late to the party, my players just went through chapter 10, by luck they went directly to the tree, but the wizard got desintegrated, the backup caster/knolwedge guy was carrying 7 negative levels. They used ALL of their healing, they fought dyrryd while seriously wounded, and once they killed him, they realized they were in no shape to explore more to find a way to stop the ritual, so they just destroyed the tree, closing the portal but destroying cauldron (and themselves) in the process.
WE HAVE TO PUSH THROUGH !