There is a problem with your circuit and the way you have it wired when programming. You have failed to use the RTS line for Serial programming. You need to have that line connected to the RESET of the ATMega328, this is as the bootloader for programming ove rserial will not start if the IC is not reset. Also you should burn the Arduino UNO bootloader rather than the one you chosen.
Seems you clarified you were using the diode as ESD protection, thank you. It is the recommended arrangement if you have a capacitor attached to the reset line in noisy environments.
The circuit between the RTS signal and the Arduino RESET pin needs to be this:
C
RTS >>----||------->> RESET(PIN1)
0.1µF
From the same "[Have I bricked my Arduino][1]" that you linked, about 3/4 down Nicks post he mentions the use of serial programming of an Arduino
FTDI Arduino Uno
GND GND (black wire on FTDI cable, blue jumper wire)
CTS not connected
VCC 5V
TxD D0 (RX)
RxD D1 (TX)
RTS To RESET with a 0.1 µF capacitor in series with it (green wire)
What you can do if you don't have the proper serial programmer with an RTS output, you will have to manually reset the microcontroller to enter the bootloader just as the IDE says "Uploading...". [1]: http://arduino.stackexchange.com/a/13293/2944