Well it sounds like just wiring the FTDI's send and rec signals (and ground) to one of the alternate serial hardware channel would serve your purposes, the Mega has four built in serial hardware ports and the standard on-board USB serial converter uses the first port. Here is link to the serial library document that explains what pins the mega has those additional serial ports on and how you access them with the serial commands.
The part that should answer your questions is the following:
The Arduino Mega has three additional serial ports: Serial1 on pins 19 (RX) and 18 (TX), Serial2 on pins 17 (RX) and 16 (TX), Serial3 on pins 15 (RX) and 14 (TX). To use these pins to communicate with your personal computer, you will need an additional USB-to-serial adaptor, as they are not connected to the Mega's USB-to-serial adaptor. To use them to communicate with an external TTL serial device, connect the TX pin to your device's RX pin, the RX to your device's TX pin, and the ground of your Mega to your device's ground. (Don't connect these pins directly to an RS232 serial port; they operate at +/- 12V and can damage your Arduino board.)
In you sketch you just change the default serial.whatever command to say serial1.whatever to use the second mega serial channel. Example:
Syntax
Serial.begin(speed) // first (if mega) or only (if Uno) serial channel
Arduino Mega only:
Serial1.begin(speed)
Serial2.begin(speed)
Serial3.begin(speed)
Lefty