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So, if I understand correctly, you wish to create a disassmbly project?
There are already quite a few of them in progress. (Pret on Github has quite a few and there are many more.)
You could try contributing in these disassemblies. ;)
That is exactly what a disassembly is. (I probably should have defined it.)
Like in Pokered (The only disassembly I've used), there are many files that represent different aspects of the original R/B game, with images for images and .asm files for literally everything else. You can change any file, or even add another file, and compile it into a new GB game, provided there's enough space to fit everything together (Because these have limits too). It even makes a file stating all of the offsets of the GB file, so you can use external programs to edit the rom.
I think the other disassemblies are similar to this.