Changing from pin 9 and

TCCR1B = TCCR1B & B11111000 | 0x05;

to pin 5 and

TCCR0B = TCCR0B & 0b11111000 | 0x05;

generates the correct clock signal.

What ever the clock signal is for the Uno, it is divided by two for the 8MHz 3.3v arduino.