I have an application that is not too dissimilar. Update by SD card would be fantastic, especially since I have the opportunity to download upgrades via wifi. At the moment I am hoping to configure a V-USB bootloader for Calunium. Then upgrades would be possible with just a plain USB connection without needing FTDI on-board or an FTDI adaptor. Is that a possibility for you?
avrdude: stk500_getsync(): not in sync: resp=0x00
avrdude: stk500_paged_write(): (a) protocol error, expect=0x14, resp=0x64avrdude: stk500_cmd(): programmer is out of sync