If I were to run KOTS again I'd go for the following structure, or something like it-
Session 1.
#1 Kobold Ambush (either- or if you like combine the two in some way- obviously not all the bad guys).
#2 Winterhaven and roleplay- see the mayor and tasked with destroying Kobolds, already have quest to discover Cult and rescue the guy from the Dragon Burial Site.
#3 Dragon Burial site- rescue Douven (that's the one).
#4 Return to Winterhaven and either Extended Rest or on and after the Kobolds.
Next day, or else latter same day...
#5 Outside the Kobold Lair (with a few more from the 2nd Ambush if the PCs used an Extended Rest).
Session 2.
#6 Irontooth (add or more likely subtract as required).
#7 Return to Winterhaven, if they're still in a fit state to fight then straight to #8, otherwise Extended Rest.
#8 The Dead Walk Again, the Elf has pied-pipered the kids to the Graveyard, go sort her out. This will improve motivation, particularly if the PCs need more backstory- have the female Elf Range, can't remember her name provide it.
#9 Either Extended Rest (see above) or after motivational speech from Mayor, and more rewards offered (for return of those taken as prisoners by Bloodreavers (pre-empts Thuderspire)) PCs head off to KOTS.
#10 Goblin Encounter #1- Make Goblins into two Encounters, the first lead by Hobgoblin Torturer- use some all or many of the combined Goblin bad guys present.
#11 Goblin Encounter #2- lead by Balgron the Fat- use some all or many of the combined Goblin bad guys present. Note PCs can avoid this encounter entirely if they manage to contain Goblin Encounter #1, although it will leave their exit blocked at a latter date.
This also gives you as a DM a bunch of wandering monsters to use as you see fit.
PCs should definitely be Level 2 by now.
Session #3
#12 Undead Encounter- combine Skeletons, Zombies et al from all three encounters (Maze, Secret Chamber & Catacombs) have them attack in waves, and be very mindless so the PCs get the chance to destroy a shed load of them- they are for the most part the shambling undead. Lessen the strength of the Glyphs if you think they will get in the way.
Have Sir Keegan follow the Undead out and if needed stop the fight- and move straight into the Skill Challenge (which can be made easier).
Fail Skill Challenge and the Undead either fight on (all now Minions) except Sir Keegan, and the PCs get Aecris only if they defeat him.
Pass Skill Challenge get Aecris and possibly whatever Undead are left (Minions) now follow the sword-wielder, Sir Keegan gets to rest now.
#13 (Without Undead followers) Combine all Hobgoblin Encounters into one fight, probably best having initial Hobgoblin Guards and Spider, and then a few more join them- including Lieutenant (not too many- Grind warning).
Alternative
#13 (With Undead followers) As above excpet more Hobgoblins present and Undead automatically Hit- they're the old guardsmen, this is home turf- they're doing what they were supposed to do...
Most, if not all of the Undead followers should be destroyed here.
#14 Trapped Statue.
Session 4.
#15 The PCs probably want to take an Extended Rest about now, personally I like to try and kick them when they're down- so I'd add a meeting with either Balgron and his boys (if they were left alive) however the Goblins flee if the going gets tough, or else for a harder challenge have the Cube and the Corruption Corpses come calling.
#16 PCs take Extended Rest.
#17 Ghoul and friends- bulk out if needed with Undead not used from elsewhere, make sure the Clay Scout gets away.
#18 Cathedral of Shadow, as is or else add a few more unsavoury creatures, maybe make the Orcus Underpriest an Elite.
Try and get the PCs to Level 3 by here- and have them Level up via some narrative conceit, 'as the last creature in the Cathedral of Shadow dies the place is cleansed- the blood stops running, screams from below... and the PCs level up, but don't get the Extended Rest just the new powers.
These last three encounters from the Extended Rest should be PC Level +3, Level +4 & Level +5 (or more), something like that anyway.
#19 The Shadow Portal, as is... except I'd look at the Phalagar (which cannot be killed- only banished via the Ritual Skill Challenge) from Thunderspire.
Kalarel should be dragged into the Portal- still kicking and screaming at the end, Orcus's Exarchs voice provides the 'you have failed me for the last time... as for you... I'll be back.'
And goodnight.
Note if you had the Mayor of Winterhaven talk early in the piece about the missing villagers then the quest continues straight on to Thunderspire.
The critter encounters on Level 1 can be used (one of them ideally) if the PCs need to clear a bolt hole to take an extended rest (they find the secret chamber within), else- ditch 'em.
Happy hunting.
Cheers Goonalan