Can you confirm that the auto-reset works?
If you've loaded Optiboot on the 644, the builtin LED (do you have one? Maybe connect one up temporarily to wherever the MightyCore bootloader thinks it is), it should blink rapidly three times each time the CPU is reset, including at the start of a sketch upload. (though I guess if you have JUST the bootloader loaded, it'll do those three flashes continuously, every one second or so.)
Are you sure that TX/RX aren't swapped? It's a common mistake, but I can't quite tell from the pictures. (neat wiring job - better than average use of colors!)