I would reflow solder on the LCD header, the shift register IC and the headers for the button board.
Yeah the SD card image has everything on it to make it work, and it looks like it has booted and flashed the AVR firmware automatically as it should have. Just need to go over the LCD header and shift register connections (RS, E, D4, D5, D6, D7) because you've got either a loose connection on one of them or a short between pins. The green LED is indicating correctly which is also driven by the shift register, and if you press the left button it will probably go out and the yellow one will come on, indicating a good connection to the shift register. Just need to check between it and the LCD. They all look like they could use a little more solder and the LCD ones look like they could use a bit more heating time because they're not really flowed there.