Ok, so I was thinking (and this is a suggestion). What if we had a site and/or tool of some sort that would allow you to download a bsdiff (or some other diff) of the latest build, then have it generate a bsdiff between the modified build (since, chances are, builds may or may not pass during user development) and the new additions, basically allowing for a pull request system to get only the modified bytes that pertain to the pull request.
Also, some sort of offset allocation system would be good, so you can reserve a range of bytes, do your hacking, and then free up any leftover free space. That way you don't get patches/diffs that have conflicting memory. I'd say 0x720000 - 0x810000 (or more) should be reserved for maps/tiles, since A-Map kinda does memory allocation automagically.
Overall, a set of rules needs to be set up to make this hack successful and organized. Once the organization is set up, hacking would commence. Of course, we also need to establish a storyline and tileset (in needed), and other stuffs for this hack, and what will and won't be allowed to change.
However, it's your show Darthatron, so you can decide what you want. This is just my hypothetical perfect organization theory here. :P