From my understanding your System Menu is still working.
What seems to have happened is that you rewrote some of your cIOS with stubs.
You'll have to:
1. Use DOP-Mii to restore the Trucha Bug on IOS36
2. Use DOP-Mii to remove the IOS Stubs
3. Use Trucha Bugged IOS36 to install Waninoko's cIOS...