Fixed the boot process!

You can now take my init.thunderg.rc and init.thunderg.usb.rc files and remove the custom init.rc file. All the new CyanogenMod root / adb permissions work.

note for the future: to use apps which need root, or to use adb as root you'll need to enable this in Settings --> Developer options --> Root access. If you try to use the 'adb root' command it'll fail and tell you to change the setting above.
The dawn of mobile phones
Ericsson GA 628 => Nokia 5110 => Siemens C35i => Siemens C45

The age of colour screens and polyphonic ringtones
Motorola C350 => Sony Ericsson T610 => Sony Ericsson T630 => Sony Ericsson K790i => Sony Ericsson T250i

The age of Android
LG Optimus One => Sony XPERIA J => Sony XPERIA SP => Sony XPERIA Z1 Compact