That's hard to say due ATmel chips want to have programmer that is specific for them. Any ideas what is model/maker of your JTAG programmer. You can always try if jtagice/avrdude recognizes your programmer. Also JTAG is usually using different pins, on mega board there is no pins specific for JTAG tho Atmega1280 do have a JTAG interface.
ATmega datasheet says: Programming through the JTAG interface requires control of the four JTAG specific pins: TCK, TMS, TDI, and TDO. Control of the reset and clock pins is not required.
PF7 ADC7/TDI (ADC input channel 7 or JTAG Test Data Input)
PF6 ADC6/TDO (ADC input channel 6 or JTAG Test Data Output)
PF5 ADC5/TMS (ADC input channel 5 or JTAG Test Mode Select)
PF4 ADC4/TCK (ADC input channel 4 or JTAG Test ClocK)
So it looks like you need to connect totally different pins on cpu to use your programmer... Maybe be easier to go on sparkfun and get one of those Pocket AVR programmers.. They are cheap and works great :)
Or if you happen to have atmega328 based boards like arduinio mini pro, arduino duemilanove or similar, you can make them work as SPI programmer too..
Thank you so much, unfortunately it did not work. I think my crash was so fatal that it broke the APM. I already have a replacement but i have yet to test my shield. Under a magnifying glassi noticed the leds shattered =(. Would it be safe to test it with my new APM?