This seems to be less a problem with JSON and more a problem with Javascript itself. What are you planning to do with these numbers? If it's just a magic token that you need to pass back to the website later on, by all means simply use a string containing the value. If you actually have to do arithmetic on the value, you could possibly write your own Javascript routines for 64-bit arithmetic.
One way that you could represent values in Javascript (and hence JSON) would be by splitting the numbers into two 32-bit values, eg.
[ 12345678, 12345678 ]
To split a 64-bit value into two 32-bit values, do something like this:
output_values[0] = (input_value >> 32) & 0xffffffff;
output_values[1] = input_value & 0xffffffff;
Then to recombine two 32-bit values to a 64-bit value:
input_value = ((int64_t) output_values[0]) << 32) | output_values[1];
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