I have done some testing with the PWM, I just built up a two pole RC passive filter, with 1k and 10k resistors and 10uF capacitors (just what I had around). PWM is 4 kHz in the end. Output is not perfectly clean, I'll have to do some measurements. I had the arduino read a potentiometer and generate PWM modifying duty cycle acordingly.
I have measured the 5V derived by the Arduino from the 8V. There is a lot of noise when the Arduino is on (off when pressing reset), see screenshots. I have connected the filtered PWM to the PSU on the perfboard, see some measurements below, that is with the 12V fan on (separate 12V rail, as I measured, better to keep that separated) , PSU and Arduino running from the 8V rail. I have to do more measurements and improve the test setup, which is not the best with wires running all over the place.
Juan