1) You should just be able to delete the files in DTW, removing them from the disc. When 20XX tries to grab a custom stage at random, it'll generate a number, check if a stage with that number exists (e.g. Gr.Iz.
3at), and then if it doesn't, it'll just try again with another random number. Not sure about the debug menu aspect; haven't looked into it.
2) The latest tech for Sword Swing Colors involves including the color information within the character's costume .dat file. A custom code then reads this data and modifies the swing colors accordingly. (This method has a lot of advantages of the older methods of changing one or two static values in other files.) This is why when you replace one of the default 20XX 4.07 custom costumes, that costume slot will [usually] no longer have custom sword swing colors. Most costumes don't have this, so you'll need to add it in yourself. You can find discussion and details on this
here. Don't forget to
edit the file's length attribute in the file header for any files you add this data to.
3) I'm not sure what you mean. If you want to replace a texture in one file with one from another, but they have different dimensions, you just need to edit the source texture to have the same dimensions as the destination texture so that you can do the import.
The colors for that are stored in a look-up table, explained in the spoiler
here. Except the table now starts at 0x3a3c90 in MnSlChr.usd, rather than in the DOL.
I thought about a 'View CSP Trim Colors' feature in DTW, which would show you the currently set colors and allow you to edit them, similar to the 'Generate CSP Trim Colors' window. But the idea was always a low priority so I never got around to it.