You can change with S3pe, via the Grid option, the valid gender, age, career and such.
But if the meshes don't fit, because they are not made for the other gender or age - then you must live with the look.

Long story short, he uses he/him but he's stuck in a female body b/c plot reasons - so I thought I could make that work by using female clothes for his whole body to give him a female mesh and use the neck fix accessory to connect his neck to his body - and I did that, and after I'd given him female mesh clothes for every single category, when it went to the household picture screen I discovered none of that had actually saved and all the clothes I'd given him had glitched back to male mesh clothes

Which is weird b/c the other thread linked said accessories didn't work but clothes and hair work just fine

If they aren't falling off in CAS itself like the accessory issue, it's possible it's Dresser's Check Outfits invalidating it this time. I think you can set specific sims as Protected by clicking on them and selecting NRaas > Dresser > Sim > Protected.

Sounds like a unique playthrough, I hope you find a way to make it work

No, they are falling off in CAS i think

and thanks, yeah it's kinda frustrating

Did you try to change the gender means add male to these specific female items with S3pe CASP Grid, so they are VALID for both?
If you have them in package format.

I don't know if you used Cardinal_Sims method, but also here the CASP files need this to be truly valid.
Then you would not need the MC CAS setting at all to make clothing available for other gender or ages, because they simply always are

I really don't know how to tell which item in-game matches to exactly which package in my files - is there some sort of tool you can use?

There are a couple of NRaas functions that can dump the instance ID for you, which wouldn't tell you the package it lived in but would be valid to use in that XML when pointed at the folder the package was in.

Dresser's Log CAS Parts will dump a log about everything in a sim's currently worn outfit.
You can also right-click items in MC CAS to generate a ScriptError that contains the instance ID. I think there is a max to how many ScriptErrors can be there at once, so you might want to have the game in windowed mode and delete them as you note the IDs.

Another way is that all CC, once viewed in CAS at least once, generates a thumbnail in the Thumbnails folder CASThumbnails.package. The Instance of the THUM is always identical to the instance ID of the CASP it is for.

I would also say just as future reference, that using so much CC that one is no longer familiar of what it even is can creep up as a number of issues. It is sometimes worth going through things and familiarizing yourself with what you are modifying your game with, sooner rather than later. It's not a priority for everyone, but I'm pretty sure my hair would fall out if I couldn't look at everything in my game and know what it was by name

with packer you can locate the file via instance number.
With the number use it in the packer search tool.

You should organise it in subfolders, male and female seperated, the category, what part, so finding it is much easier.
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