OK I built and started testing out my breadboard arduino clone. I had two mistakes but they are easy to fix so next revision will be perfect 
Managed to program the bootloader using the 6-pin ISP cable and then uploaded sketches that blink the red LED and also send/receive data using a USBmini-type thing as well as a USBttl cable from mouser
you can see more detailed photos on arduino | Flickr
