Debugging tools in n64 emulators (such as nemu64) are sufficient to make tracking down particular game logic more in the neighborhood of a fun puzzle than a slog through (roughly) a megabyte of assembly. Super Mario 64 in particular has had an active ROM hacking community for over a decade, so there is a large body of knowledge about the game's internals, though it resembles folklore more than a systematic approach. The hard parts to discover through disassembly are the 3d graphics api and memory-mapped IO, but that was already worked out quite a while ago for emulators (based largely on patent documents).

In fact, there are level editors for SM64! Kaze, the creator of this hack, occasionally streams development on twitch; it's a lot of cross-referencing different pieces of accumulated documentation.

Edit: An example of some of the documentation, a list of ROM addresses of various textures: http://wiki.origami64.net/super_mario_64/textures