I’d always suggest that you un-comment one of the board types and check that you are aware which pins are being used by Edgent in Settings.h, and probably add those to this list as comments so that you can see your pin usage in one place…
More info on that here…
You won’t get full brightness unless you use 255 as your maximum with 8 bit resolution. Also, it’s duty cycle not voltage that you’re measuring, so unless you have an oscilloscope available you won’t be able to take any sensible measurements.
I’m not clear why the logic level converter is required, what the specification of your LEDs are. Generally speaking, you would design your circuit so that you feed your MOSFETs with the desired output voltage for the LEDs, then drive the MOSFETs so that the full voltage is delivered when the maximum duty cycle is applied.
Your flickering is probably also caused by your circuit design.
Pete.