Situation normal, all O.K.

...... The frame on the bike acts as the 'second wire' to make the various circuits work. While Black/Red/Brown make connection to the + battery pole, the frame and motor are connected to the battery - pole to complete the circuit. Really you have just tested the ground paths on some circuits.
If your bike was 'grounding-out' then the main fuse (15A) would blow....
To achieve ' no continuity' from say, the black wire to ground you will have to disconnect the coils, the headlight ( if 'on' ), the tail light, the running lights ( if present ), the N light, the oil pressure light the black wire @ the regulator,........... what I'm saying is that Black will always show continuity to ground unless you disconnect everything connected on that circuit.
You haven't said what's wrong with your bike in your post?.... does it run, not charge or something ?