When you say 3.3v .. is that exactly 3.3vdc or 3.4vdc ? Does it need to be more or less .. what is the ideal voltage? How much does the 5vdc affect any of this and what setting is ideal?
Here is what you need to do for the most accurate voltage setup:
take the top case off of your DIMM board and find ground and VCC points on some of the 3.3V chips and the 5V chips.
then, while measuring the voltages on these points adjust your PSU up or down until the 3.3V point = 3.31V and the 5V point you found = 5.01V
This will give you the most accurate PSU adjustment possible. When You suspect voltage issues you should ALWAYS measure from one of the ICs that is actually utilizing that voltage, because ultimately that's the only thing that matters. on a NAOMI this should be on the DIMM board because it's the furthest removed from the power source.
for fun you can go back and measure the voltage at the power connector and you'll likely see 3.4 and 5.1V respectively. There can be quite a bit of power drop between the power connector and the ICs that actually need it.