And check if your USB loader supports Ocarina, as you'll need it to run codes.
Most loaders do support Ocarina, but you may have to turn in on in Settings.

Loading from a USB is the same as booting from a disc.

And since Riivolution doesn't support backups, you have to use the File Patch Code.
For sounds, you'll have to directly insert the .bsrar into the .iso.

I thought the DAE -> MDL0 converter wasn't done yet.
How do you expect the models to work in Brawl?

They go in the same place textures do.

There seems to be a limit on only 37 extra stages, due to the fact that only a certain amount of stages are allowed on a single page (or something like that; I can't remember the exact numbers).

Jizzus, what did you do to make the file size so large?

I don't know the actual limit, but my mu_menumain has a file size of 4.06MB

Mmm. You can remove Bowser... but I don't have much knowledge about the subject.
Someone else may be able to offer more help.

The main problem is that the Bowser you fight is just that: Bowser. If you happened to change the fight so you fight Giga Bowser, you're essentially fighting the Final Smash.

So if you wanted to fight a "knockbackable" Giga Bowser, you would need some sort of moveset for Giga Bowser (like Eldiran's "Killable Giga Bowser").

By the way, even if you somehow managed to edit the correct files as you needed to, you would still need to:

1) Boot through Riivolution (only you're using a retail disc. required every time you boot the game, just like Gecko)

2) Boot through Gecko (File Patch Code needed to use your modified files. essentially, you're doing what you did when you were using the codes).

or

3) Install the modified files directly into the game and load the backup from a disc/SD/USB (this requires a LOT of rather confusing work, so this is the exact opposite of what you're going for).

Would it be as simple as putting something in a hex editor?

What.

Anyways, the reason you need the code is because you're not supposed to be using Independent Pokemon in the first place. When you do, their results data can overwrite other parts of the game, which can lead to a corrupted save file.
So unless you know how to get around that (basically changing how the game works), you're stuck with the incredibly tedious process of having to boot Gecko to load the codes.

You can try to modify the actual game files.

Codes are just used to get around that sort of stuff.

Good luck.

Please.
Read.
The.
Sticky.

Har. Had no idea about the polygon/face thing.

...Anyways, would the lag have to do with the vast amount of polygons?

2GB is the limit.