It's silly that no Any Title Deleter apps support Gamecube, read somewhere that it was planned by red Squirrel maybe in the next release but that doesn't help you right now.
On 4.2E you really need to stick with installing 4.2 System menus as downgrading is problematic.
-1035 errors are due to missing/corrupt cIOS.
-2011 errors are due to missing cIOS.
Your cIOS might have been removed upon re-installation of System Menu 4.2.
I wonder if IOS249(cIOS38r14) cannot be installed via Wad manager via IOS36.