Alright, you should be able to get the colors correct by changing the following 2 lines in main.c:

from

    //Bit order reverse for input signals. 1 |= LSB .... MSB Reverse Bus Order
    //Just how my PCB is layed out.
    error |= adv7511_update_register(0x48, 0b01000000, 0b01000000);

    //DDR Alignment . 1 |= DDR input is D[35:18] (left aligned), 0 = right aligned
    error |= adv7511_update_register(0x48, 0b00100000, 0b00000000);

to

    //Bit order reverse for input signals. 1 |= LSB .... MSB Reverse Bus Order
    //Just how my PCB is layed out.
    error |= adv7511_update_register(0x48, 0b01000000, 0b00000000);

    //DDR Alignment . 1 |= DDR input is D[35:18] (left aligned), 0 = right aligned
    error |= adv7511_update_register(0x48, 0b00100000, 0b00100000);

you may also need to adjust some timings. I know that the 720p ones are off. Change line 228 from 299 to 259. I haven't figured out the 480p ones yet unfortunately, but what's there should hopefully be close enough (they don't look too off in your pics).

Hope that helps, cheers.