Sure, it says serial port because it talks to the FTDI chip directly, and not the Arduino.
The avrdude line says the chip isn't talking.
I already mentioned you can't connect Vcc to Vin, it needs to connect to preferably the green PTC device where USB power comes in, or to the 5V header pin.
Vin goes thru the regulator, and you won't have 5V at the uC anymore.
Once you have good 5V around the board, try swapping the Rx/Tx lines if its still not talking.