Did I understand correctly:
- No (R) and (L) for starting camera
- No touchscreen
- No Circle Pad and Dpad
inside Home Menu while all buttons are working in GodMode9?
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Try touch calibration inside GodMode9 to see if the touchscreen works.
This strange behavior can be caused by permanent touch input (dirt, bad digitizer). Carefully (!!) try to clean the edges of the touch screen. Make sure there is no dirt between digitizer and frame. Don't use metal objects as they will pierce the digiziter easily.
If cleaning does not help you can disconnect the touch panel from the motherboard (until you get a replacement). The N3DSXL should work normally with missing touchscreen (but makes some games unusable).
Good luck!