Main fuse clicking HELP

I have a zx900 A2 project bike. I just put in a new main wiring harness( the old owner told me there was a short in the old one) put in a new battery and all the proper fuses and no problem everything turned on and the engine spun so i put it away for a few days( due to rain and new parts arriving) and i go out to check the bike everything is dead the battery is reading 4 volts and the acid is gone and all i hear is my main fuse ( part # 056700-5260) clicking so i get a replacement and all i hear is the new fuse clicking. what do you think it could be and what should i do??????

* Before i put in all the proper 10 & 30 amp fuses the main fuse kept blowing and he last time before i replaced the fuses i heard the crack of a wire burning near the motor and saw a little smoke. I checked everything and i saw nothing to bad just one cracked plastic case so i taped it to reseal it and once i put in all new fuses there was no problem.

The clicking is probably a relay & that may have something to do with the battery.
Is the battery new? And was it properly filled & serviced prior to installation?
I didn't see that main fuse part number (56700-5260) in the Electrical diagram for your bike.

You should get a wiring diagram & investigate the smoking wire & any components related to it.