Just relooking over the encounters, I'm sure they would have less padding (no goblins, iron defenders, ochre jellies, etc) to fill the XP budget. Turning (esp in Pathfinder) would eliminate a lot the weaker undead, and ranged/magic attacks would be more important. A lot of the adventure was a pain trying to spend the XP budget.
That's not my reading of the adventure at all. My reading is that you wanted to pad what is essentially about a half-level adventure into a full level.
Turning the adventure into a scene based one, we have:
Pre-credit sequence: The hooks.
Scene 1:
Addressing the Wild Rose. How the PCs do this is up to them - a 6 before 3 structure behind the scenes works, but this is a scene. If the PCs make it through they gain XP accordingly.
Scene 2: The Dark Knives Guild. The PCs know Duval was a member - and need to find out where and how he lies. If they botch this but have mentioned they want to find out where Duval lies, they get the combat - with the combat opening something like "You're looking for Duval's body? You're about to join him in the old crypt." Textbook example of Fail Forwards here.
Scene 3: The Complication. I'd base this on either the Dark Cabal or The Forgotten Dead - preferably the Cabal. Using the Dark Cabal version, with Duval around, undead are easy to raise, so the Dark Cabal has based itself here. They can be fought (they have treasure) or sneaked past as a group - but run the risk of being reinforcements for Duval. Terrain here: broken gravestones and open graves. If the PCs sneak past (or bluff/intimidate) each failure means that Duval gets a reinforcement from the Cabal attacking the PCs in the rear.
Scene 4: The Crypt. The Complication was near the entrance to the crypt. Duval is inside the large, open ossuary with skeletons sorted into piles by bone type. And some assembling themselves into literally a dozen decrepit skeleton minions. The skull pile bites anyone who passes through them (including Duval).
Epilogue: As before
The whole thing would at this point be worth half a level or so and could be run comfortably in a couple of hours.
Your version has, in place of the section of the adventure I called the Complication:
Rotting Welcome Party (L3),
Dark Cabal (L2), The Forgotten Dead (L1), Foul Things Grow (L3),
Scavengers (L2), and
Rat's Den (L3). Possibly also
The Crypts Come Alive (L6). Not one single one of these encounters is more than extremely tangentally relevant to the plot of the adventure; they are merely there from your description so the PCs have half a level's worth of random monsters there to grind against for XP.
Put half a level's worth of random monsters into an adventure to make the PCs grind for XP and guess what? The PCs will feel as if they are grinding for XP.
The table on DMG p104 you were following says over the course of a level that the PCs should face an approximate mix of challenges; it doesn't say or even imply that this has to be one single adventure.
Edit: To sum up, the design process seems to have been.
1: Write a basic plot.
2: Pick a map at random
ignoring the guidance in the DMG.
3:
Add as much XP in the form of pure grind (monsters that are there for no other purpose than to be killed for XP)
as was present in the actually necessary parts fo the adventure.
4: Blame 4e when points 2 and 3 don't work.
Explain to me in which editions points 2 and 3
would be a good idea please?
Sadly, by then it was probably too late for more than a fair share of players.
What doesn't help is the number of people who spread misinformation about 4e.
More constructively: why does 4e work poorly for dungeoneering and how can it be improved for such?
4e combat is big and cinematic. This is great for epic fights but not terribly good for dealing with an orc guarding a pie (4e dragons on the other hand seriously kick ass). There are two things to do.
Firstly: Minions and area of fights. I believe that at least one 4e conversion handles the entire Gatehouse of Hommlet as one single encounter full of minions.
Secondly: A Quick Combat Resolution System where you can wrap things up in only a couple of rolls. I've a homebrew where for unnecessary and one sided fights, or for serious pants-round-ankles ambushes damage is applied directly to healing surges. (PCs and monsters do 1hs of damage each - strikers 2, rogues 3 if they haven't attacked the previous round, leaders can prevent 1 hit, defenders get an interrupt attack, controllers attack 3 separate targets - most monsters have 4hs in this system and unaware* monsters take +50% damage, round up).
* Unaware isn't merely surprised. A monster or PC expecting trouble is never unaware; a guard dozing in a guard box or someone who's just sat down to dinner is unaware until either they have been hit or the end of the first round.
Edit: And to support Kraydak below, making attrition matter is the purpose of having damage go straight through to healing surges. Dungeons have been broken ever since the near-elimination of the wandering monster tables allowed wizards to recover their spells in the dungeon (one of the things they were there to prevent). 4e just made this carry through to hit points (which weren't a problem in 3e with wands anyway). Extended rests work IMO much better if they are narrative-appropriate rather than just a sleep for a few hours.