I am in now way offering any helpful information due to me being semi new to the scene. However I read over your post and I am wondering something....
1 You said: "I guessed that the boot.dol in the CFG USB Loader Folder might have been the same thing as the WAD (I was tired) and uninstalled that as well. When the Uninstall was complete" I don't understand how you uninstalled the boot.dol from the cfg Folder... What program did you use?
Your .wad file to uninstall the channel should have been in SD:\wad
If you didn't remove any IOS's I don't see why you are having an issue. Did you remove the boot.dol from the Root of your SD card?