The order is mostly flexible, but I suggest the following order.

(Optional:
Kobo Touch Hacks for telnet, ftp, and user script on startup.
Followed by the inverse mod. The inverse mod MUST come after enabling telnet, ftp, and the user script since it modifies the startup script automatically.
)

KoboLauncher first, since it facilitates testing.
Ensure KoboLauncher works.
koreader next, since it must be installed before it's files are modified.
Now for muness' KoboLauncher.sh modifications.
Verify that the launcher icon loads koreader.
Now for the cgm mod.
Verify that the cgm mod works.
Now for the xor mod.
Verify that the xor mod works.
Finally, apply trekk's configuration.
Verify that trekk's configuration works.

I'm not up on all of the other mods.