The problem is, you are not studying the example. Because you won't do that, your code does not work.
Again, here is how it works in the fht_adc.pde example:
for (int i = 0 ; i < FHT_N ; i++) { // save 256 samples
while(!(ADCSRA & 0x10)); // wait for adc to be ready
ADCSRA = 0xf5; // restart adc
byte m = ADCL; // fetch adc data
byte j = ADCH;
int k = (j << 8) | m; // form into an int
k -= 0x0200; // form into a signed int
k <<= 6; // form into a 16b signed int
fht_input[i] = k; // put real data into bins
}