setting amplifier gains

If you're going to use that method by itself you have to make some assumptions:  one is that the power output that the amp is rated for is what it truly is in your installation, and two is that the net load is exactly 4 ohms.  Either or both of these can be off.  For example, if the actual net load were 4.3 ohms, the result would go up to 58+ volts if you used 800 watts as power in the formula.  And so on.

Because of this, you should also use the listening test.  With either method you have to 1) use test tones in the frequency range of the subwoofer, and 2) have the volume level of the head unit at the highest output just under clipping level.  The test tones should be recorded at a reference 0 db level.  This means that the deck output must be tested and set before the amp gains are set.

When you hear the tone change to a clipped tone and then have turned the gain back down enough so that the tone is pure again, read the voltage output.  You will probably find that it is much closer to the specified power than what you found.  But if you again find a good, steady reading that is higher, then the power output may be more than specified.  You won't really know without doing a complete bench test, but you will know that the gains are set right.  The relative position of the gains (..."set at 1/3"..) has nothing to do with anything.