I'm a little confused.
You blew a couple of fuses, and the wires still smoked?
Which live wire did you forget to unplug?
The only thing i can think of that happened with the smoking wires is that the wire either was not fused or not fused properly. If you use a 200 amp fuse that is powering a 16ga wire at 12 volts, chances are that wire will smoke when short circuited.
The reason for your midrange not working is questionable. It sounds like the heat from the burned up wire seared some other wires, which would cause you to have to replace "a few fuses".
When you sear two speaker wires, the impedance goes through the roof. A headunit can only drive a certain amount of impedance and survive.
You may have to rip everything apart and take a look at the damage that was done.