Are you sure you want to execute the second loop 15 times? o.0
I'd have guessed you wanted this instead:
// Clock Cycles 2-16
for (int i = 1; i <= 15; i++)
{
digitalWrite(clock1,HIGH);
delayMicroseconds(4);
digitalWrite(clock1,LOW);
delayMicroseconds(4);
controllerData1[i] = digitalRead(data1);
}
for (int i = 1; i <= 15; i++)
{
digitalWrite(clock2,HIGH);
delayMicroseconds(4);
digitalWrite(clock2,LOW);
delayMicroseconds(4);
controllerData2[i] = digitalRead(data2);
}
}