There's a great podcast I started listening to before running it called Tabletop Gold which can really help you see how the adventure can play out, as well as some cool twists you can incorporate into the story. It's a delight to listen to as well.

I'd also recommend from my own experience working with your players to come up with backstory connections to the town of Otari and to the city of Absalom. The adventure is primarily set in Otari, and it features an existential threat to Absolom as the main driver of the plot. When I started the campaign, I told my players that they needed to include in their backstory some kind of personal connection to the city of Absolom, as well as a reason for why their character is in Otari.

Depending on how much you pull from Troubles In Otari (and if you started with the Beginner Box), you will find the party is over levelled for the content unless you use the slow XP track. This will make some of the encounters trivial and some of the more difficult encounters average. I’ve been running it for almost a year now and the party has just reached the fourth floor and had a fair bit of trouble with one of the significant encounters there. They’re about 2/3 of the way to level 5 and could barely scratch the enemy, though they came up with an ingenious plan to pit two creatures against each other. Even then, it was still a difficult fight. Had we been using the normal XP track, they’d likely have been level 6 for encounters that are tuned for level 4.

Some more advice would be to flesh out the town NPCs a bit more (the expanded PDF helps with this). It gives the party more reasons to go back to Otari, can help break up the dungeon crawl, and allows you as the GM to raise the stakes by having those NPCs impacted by certain events.

As for PF2E in general, the mechanics work well. Try to emphasise to your players that standing still and attacking three times is going to make them a sad panda. Encourage them use of skills like demoralise, feint, and combat manoeuvres like trip and grapple. Stacking status and circumstance bonuses/penalties will make difficult fights a lot easier due to unbounded accuracy. PF2E is heavily focused on party composition and tactics rather than min/maxed individual efforts.

The biggest problem I’ve seen is that so many of the rooms are very small, making for cramped, awkward maps. Sometimes our group calls it Abomination Closets, it’s so cramped.

I’ve seen suggestions that you double the size of all maps but I’m too lazy for that.

Other than that, I have very few complaints. It’s reasonably well-written and the difficulty tuning is good, assuming a party of 4 at the correct level.

My group is about 30-40% of the way through, so I can speak from experience about the later parts of the campaign. But so far we are enjoying it.

It's a combat-heavy campaign as written, so if your party wants to just roll dice and smash things, you might be fine running it completely as is.

My group is more focused on mystery solving and roleplay; they get more of a kick out of piecing together what happened down there than powering through baddies. One of my gripes about the module is there is a huge amount of back story that's given to the GM for each area, but few suggestions on how to get that information to the players. I've started to tailor some encounters to have more options to use stealth or talking to avoid encounters and/or get more information, as well as adding things like old notes and letters to find.

The other thing I've found is, as written, the Vaults can feel very static. The players can clear a few rooms, leave, come back, and everything is where they left it. If you want to making it react more to a party rampaging around, it will take additional work.

Abomination Vaults Expanded (https://www.drivethrurpg.com/product/418672/The-Abomination-Vaults-Expanded) is one resources I've been borrowing ideas from to adding bulk to the campaign, and might be worth looking at.