1) It could be that you installed the new forwarer channel, which requires IOS58. Install it, and use the hackmii installer to reinstall the HBC and see whether that fixes it. To install it as app, you merely need to copy it to the apps folder with your pc.
2) don't know this one.
3) nope, system menu 4.1 is the ideal system menu.
4) Maybe you used another cIOS?
5) USB Loader GX 2.0 seems to work fine for most.