Based upon the OOT Debug ROM scene and entrance table extension hack, I created a program to extend these two tables and fix the pointers to them automatically. Additionally, due to a point brought up in the brief discussion regarding the limits on how many new files can be added due to ROM size limits after posting about the aforementioned hack, I wrote up a few code segments that would allow Yaz0-compressed files to be stored in the ROM and decompressed in real-time as needed, similarly to how MM operates.
The idea is that, when intending to start work on a mod, you would run the ROM through this program beforehand. Any new files added to the ROM, of course, will have to be added to the look-up table that this program produces at the end of the ROM; I intend to write a small helper program for inserting new files, but that will have to be done manually. Please consult the readme for more information, or ask a question here and I'll do my best to answer.
Windows 64-bit binary: https://mega.co.nz/#!llskDQ6D!9mZacQQ-u2XIMFW70yJ-y8hShMnJ0NNAvy_ASeE0AVE
Source code: https://mega.co.nz/#!oh9zgYSA!UmWufyzsgRUIEGyCdo2Gh-vC66CXFS6gpo-7Fwudj9E