Howdy everyone, just a little update.
The project saving/loading speed up is done and working (with some caveats).
What I implemented was, if a song is not in use, all of the files related to that song are not written when saving. This speeds up project loading/saving by quite a bit (there are 23 files written out for each of the 16 potential songs). So, if you only have 1 song in your project, 345 fewer files are written to disk. Same goes for loading, 345 fewer files are opened and read. If you add a song to your project, those files will show up when you save. I've been doing a lot of testing of saving/loading/renaming etc. A little more to do, but so far it's working like a champ.
In general the disk I/O is
super slow on the MV. I plan on looking at that in the future, both at the HW level w/ the IDE settings and the FAT filesystem code (which is hideous).
What took so long was trying to get the actual song *directories* to not be created. This was a HUGE can of worms and I spent the past 4 or 5 months just on that. In retrospect, it was a colossal waste of time. I have OCD and it bothered me those directories were there. To get that working entailed modifying a lot of different places in the existing code (which is super tedious due to the code not being position independent). Just a ton of extra work for very little payoff. I backed it all out. I'll just ignore the empty directories.

If at some point in the future I discover an easier way to do this, I'll implement it.
The only thing I should add at some point is the removal of those files if you delete an existing song (other than the first one) from your project. As of now, if you remove a song from your project, the files will stay, so project loading/saving will start to creep back to the original speeds with each additional song added/removed. Worst case would be using all 16 songs and then removing all but 1. The files can always be removed manually over USB, etc.
Additionally, copying existing projects will not remove unused files. If you know your project doesn't use the files, they can be deleted and things will still work normally.
I am curious if anyone uses more than 1 song in a project, I never do so this is a huge workflow speed up for me. It's 1 song per project for me.
There are more optimizations I can do here, but I'm going to move on to something more interesting for my next change.

What's also good about my firmware changes is that I'm pretty confident it won't brick MV8800s. You can very easily go back to the original firmware (I have done this hundreds of times over the past year or so). The reason why is because I have not modified the bootloader at all which is what handles installs, etc. I say all this but when I do make these changes available I will still have to make note that I can't guarantee things and can't be responsible. But that's the usual way with custom firmware.

I'll make another post when I've decided what to tackle next! I really want to implement varispeed, but I have been talking with the fellow who makes the MV-OP1 ADAT card and it seem I may be able to build a circuit w/ MCU to do it in hardware with minimal software changes (if any).