Now, some apps (idk what you would call these, i guess non 'build-in' apps) are accessible via USB flash and there icons can be extracted by reading from 0x1000. I've already extracted some of these. My question is, where are the icons for built in apps (ie run matrix, system) stored on the calculator.
At some point I might want to make a custom shell/menu and it would be useful to be able to display these icons (without having to screen capture and use sourcecoder on all of them).

Those are some nice icons, thanks for extracting them!

Pointers to the icons of inbuilt apps are stored within the array of inbuilt_app_info structs also used to get the inbuilt app names and code points. It's at 0x8071e130 on OS 3.60, but you'll probably want a more stable way of finding it from assembly. It's referred to as "InbuiltApps" in my documentation and syscall disassemblies: https://bible.planet-casio.com/drcarlos/ if you want to find where it's referenced.
You can find more info on the struct at https://bible.planet-casio.com/drcarlos/Notes.html
Please let me know if you would like any more assistance!