I will address the receptacles first that is just poor workmanship for sure. Some misalignment in cabinets can be fixed with adjusting the hinges . I do not understand the issue with the shower. The hood covering what lights ? IMO the wrong hood chosen for that space who made that decision is who is to fault. You do need to recognize this is an old building and has some quirks that you just hae to live with and sometimes shims are the only way. I agree the doors under the stairs were not made to fit custom that you will have to take up with the cabinet company or maker. I renovated a 1905 home the floors sloped to the center big deal but fixable , the walls were all plaster and lath some perfect some not so much , we learned that some fights were not worth the money and honestly when were finished no one but us would ever know the issues.

1) covering lights could be a big problem. Can you change the lightbulbs?

2) The shims look like they will be a problem the minute they are knock out, which they probably will be at some point. A better solution is needed.

3) If the water drains well, then you're good. The lack of alignment with the corner is unimportant, IMO

4) I'm not seeing the issue here

5) I don't see an issue here, either. It's barely noticeable and the fault appears to be in the ceiling.

6) Shims are problematic.

7) Yeah, get them to straighten the outlets. You might compromise, if you know some of them will be behind furniture.

I'd start with your list and negotiate. Write down the issues, try to get an estimate of what they would cost to fix. Pay attention to the non-negotiables and accept that in the end, you probably won't get all you ask for. Read your agreement carefully. Read any marketing materials/website of the contractor carefully to pick out words like "attention to detail".

The electric outlets, and maybe the custom cabinetry. The rest? Shims are commonplace, sorry. You're in an old building. The drain in the shower? Seriously?!

The new ceiling ? Okay.................joint compound.

Has your final payment been made? No? Then hold it until the most serious are fixed. and leave the shower drain alone, the closet is up to you : ) might need some scribed trim

Before one sends the final payment one ususally double checks to see if the punch list items were completed. Start one. Gotta say however, if my project manager ever said to me "does it really look that bad" or some facsimilie there of, I would fire his a$$ on the spot.

The outlets would drive me nuts. That would be the first thing done. Who ever installed them, needs better glasses.

A final punch list makes sense but be realistic on what can be reasonably ”fixed“ at this point -

can you adjust the outlets?

fwiw when we were closing on our vacation build there were a few wall paint touch ups that needed to done - i ended up doing them, literally took me 20 min and created a ton of goodwill with our builder who would have had to get the painters there etc.. so he ended up doing several extra things for us at the end that i would not have been able to do -

Write the punch list.

1. hood should be reinstalled as lights are not fully accessible.

remove, fill void above tile backsplash, reinstall hood with back flush to tile backsplash. That should bring it forward some. Some hoods are not deep enough for custom cabinets but this issue should be less

2. PM should get all the plugs and switches level.

the rest I'd need to see better. shims can be normal to an install.

Ask the tile contractor to walk you through their shower pan decisions.

Really appreciate all the comments here, thank you everyone for all the insights. I'm at the final payment, but based on their behavior thus far I'm skeptical if that's enough motivation for them to address even just a fraction of the remaining issues I have.

For shims, sounds like this is something I need to live with as long as it's out of the way and secure.

For the hood, thank you for the callout about lights not being replaceable. I will definitely be pushing them to fix this installation.

For both the shower drain, cabinets, and closet it does seem minimal and I know it's mostly aesthetic, but these were predetermined signed off designs that were either slightly off (the shower drain and the cabinet angles) or completely changed without notice (the closet and the cabinet cutout). I haven't gotten an explanation on the shower yet, but for the closet they stated "we made some adjustments for usability" after I saw the installed structure which I don't completely agree with (especially since these changes were not communicated beforehand). Writing this out, it seems I've been too lenient with them in accepting something that is completely different from provided designs.

For the ceiling, this is something they tore down and replaced which is why I'm confused why it's objectively worse (more curved) than before, but maybe I'm missing something here.

For electrical outlets, agreed it's also minimal and something I can probably take on myself, but this is actually what prompted me to start this post; after caulking all the newly installed baseboards in our apartment, sealing gaps/holes throughout around electrical/plumbing/vents/etc, and then starting to adjust outlets, I started to question what I should and shouldn't be accepting as final.

those outlets would drive me nuts!

I have a couple like that and even the one hiding amongs wallpaper kills me when I see it.