Did you try it with the FTDI after the new bootload?
Have you reversed the way you have connected the TX0 RX0?
I usually bootload my 5V 16MHz Pro Minis (Clones) with the Uno Bootloader, which does flash three times when reset. You then have to remember to select Uno as the board which can be a pain. 
This may be a waste of your time, but what about loading some kind of serial sketch using your ISP programmer and then checking if your FTDI is hooked up right to receive what the pro-mini is sending. Keep in mind that you will have to reload the bootloader in order to load sketches using the FTDI after this.