Not 100% sure, but I think this is the pinout for J4. (Got pinout from a TC1 schematic) Double check by ohm metering between J4 and the Atmel MCU.
(Reset, SCK, MISO, 5V, MOSI, GND)
What I did to program my TC1 was connect Reset, SCK, MISO, MOSI & GND to the programmer. Then I temporarily jumpered out the test button to keep the unit powered up during programming.