Yes, agreed, the low frequency response is not usually where we're looking at primarily.
Also you're right that it is +/-50mV full scale is the most sensitive setting for 3206B.
I was also wondering - do you make use of the moving average filter? That increases the effective resolution of the ADC, at the expense of lower overall sampling frequency. Could be useful, maybe at low frequencies where I guess you inject a small signal due to the high gain of the control loop at the low frequencies?
(When I fire up my Picoscope software GUI, then the averaging is found under the Channel Options for that particular channel and the Resolution Enhancement allows you to increase the effective resolution up to 12 bits.)
Actually that reminds me - are you planning on implementing the adjustable stimulus amplitude across the frequency range? I think that is usual method, as I read up on the subject.
I know it's easy for me to ask, but takes time for you...
When I look at various videos of people doing these measurements using the typical gain/phase analyzer's on the market, then they are using scope probes and other cable connections that use co-ax cable, but then have either a long ground leads (in the case of a scope probe) or flying leads with hook-type connectors on the end (in the case of the cable that injects the signal from the transformer). This kind of test set-up picks up a lot of switching noise (from the dc/dc converter) and couples it right into your signal, increasing the noise. To greatly reduce this there are better ways to connect the probes into the circuit using soldered connectors. My picoscope came with some adapters that allow you to remove the probe tip and instead fit something that would connect right into a miniature BNC connector that is soldered onto the PCB. That would keep the scope shielded for right up to the PCB. The link below shows what I'm on about, but the solution used there is a bit makeshift and I think the adapters I mention would be even better.http://www.eetimes.com/document.asp?doc_id=1273282