How did you put a bootloader on the '1284?
"Connected Rx, Tx, Reset pins of 2 boards together. "
Grounds are connected also?
'328 is removed during this so it is not interfering?
Bootloaded with the clone board itself. Arduino as ISP tutorial. 
Yes. I removed the 328 from the board while uploading the program via the clone and Yes I have connected it to common power supplies (Vcc and Gnd are same in both boards) too...