I'm looking to make a new object with completely custom functionality, and would rather build it up from scratch rather than trying to untangle a mess of pre-built functionality that I don't need 70% of.

Unfortunately i'm struggling a bit due to 90% of tutorials being "Here's how to recolor an object", and documentation on the core functionalities seemingly being lost to time. I'll document it myself if I have to.

The current issue i'm struggling to solve myself is that adding resources like new CRES and GMDC nodes don't seem to save their changes. Their names get stuck as [Resource Node] and [Geometric Data Container]. When I add and edit new blocks and commit, those blocks then completely delete themselves once I leave click away from the resource no matter what I do.

What am I missing that makes these resources work? I tried adding an MMAT node that points to the CRES, but it can't locate it in the scenegrapher, probably because I can't change its name at all.

The issue is that pretty much all the resources are linked to each other in some or another way, so the easiest is to start with something that's close enough to what you want, and then go from there, deleting resources you don't need (and making sure you don't delete the wrong ones).

For meshes, when you extract them, it's usually best to extract them "all in one" from the same item, since the GMDC/GMND/CRES/SHPE are interconnected. Otherwise you could end up with a broken CRES resource, or pretty much anything else broken.

The TXMT/TXTR/MMAT are more forgiving, and can be extracted from any file, but they still need to be properly named and linked up to show properly for your file.
These tutorials (along with the linked one by IgnorantBliss) shows some of the connections:
https://hugelunatic.com/adding-recorable-subsets/ (this one in particular)
https://hugelunatic.com/making-objects-recolorable/

A full-on 2how everything is put together" is too much to type out here, though. If you poke around in an object file, you can find most of the how and what on your own. It's also a good idea to follow some of the more advanced tutorials that shows how to edit stuff you normally wouldn't for a plain object/object conversion - adding subsets (how to add texture resources properly).

In a lot of cases if you want to make "something else", you need most of the same resources as you would get by cloning something that's roughly similar to it - but you can edit most of the resources to fit your project, and you can also swap out resources (but need to make sure everything is linked up and named properly).

Hugelunatic has some useful tutorials here (sorted by level at the top)
https://hugelunatic.com/category/home/ts2-basic/

And there's an archive of various tutorials here, which could potentially come in handy:
https://ts2tutorialdatabase.tumblr.com