Moreover I checked the cable going from under the engine to the battery box and it's true it sounds kind of 'crunchy'
Yup, that is the sign of burn out wires. Strongest recommendations is to look up Drewpies rewire, from Tech (tab) down to electrical, also found on the home page,
http://www.xs400.com/forum/showthread.php?t=5934 Picture number 4, is the pic of the shot wire.