You don't have to delete anything listed in your syscheck log, it's perfectly fine. Loaders like NeoGamma and WiiFlow doesn't need official system files, but only custom patched files (cIOS). Currently you have IOS236 (not really needed), IOS249 (unknown rev) and IOS250 (also unknown rev) installed. NeoGamma only works with IOS249 and WiiFlow works with all known cIOS. I recommend updating your IOS249 with the ModMii PC application and Wad Manager to latest d2x IOS249[56] and IOS250 to latest d2x IOS250 [57]. If you want to play gamecube backups and have a compatible drive, you can install any cMIOS also with ModMii. Finally you can optionally install hermes cIOS with ModMii (but isn't really needed).