12mm glass will be good to block the old holes , you dont need to fill in the hole at all just the square piece of glass laminated over the hole. make the glass squares a fair bit larger then the hole (if hole is 2 1/4" use a 6" square etc.)and use construction grade silicone to adhere the glass, lots of silicone and trim what drys and squeezes out after with a razor blade
looking good dom lots of progress if you need any more help just pm me and i will be glad to help any way i can
cheers
denny