Uh, well you're going about this all backwards. The new ECU was pointless. The fuse is for the power into the ECU, not out of it. The fuse is there to protect the ECU from getting a surge into it so it doesn't overvolt. Your battery/wiring harness is the problem as something is shorting it out and blowing the fuse in the circuit TO it. So you need to check each and every connection you did and measure voltage in and around those connections. Throwing more money and parts at the issue isn't the proper procedure and won't fix anything. It will make it worse actually, because now there's so many new things to check it's hard to figure out what the problem is.
And you bought a new OEM Kawasaki harness, correct? I sure hope so!
And you bought a new OEM Kawasaki harness, correct? I sure hope so!