As well as my main connector there is a black plastic tube connected. It screws apart in to two parts and inside is a glass 10A fuse. It was casuing me problems starting - as in needed to shove it to get ignition lights on and then caused total electric cut out when I wis riding the bike.

If I disconnect it everything seems fine - is it safe to do this. Thanks in advance.

 

Where does the other end go? It was probably used for some sort of aftermarket accessory. There are no other wires shown on the wiring diagram.