Replicating Tx and Rx LEDs
The USB to serial and LEDs are done with the ATmega16U2 (the chip near the USB socket). 

If you look closely you'll see there are 4 pad near the chip, JP2 in the schematic. You could solder some wire to it to connect your leds. You could then slightly modify the firmware running on the ATMega16u2, and upload it using DFU.

I did this on my arduino uno to break out the reset signal, so I could use my UNO to program an separate ATMega328 over serial.

In your case you could use the pads connected to PB4 and PB5 (as the original code uses PD4 and PD5), so the you only have to change DDRD and PORTD, to DDRB and PORTB in LED.h.