Much better question, while I had the original M/M stack, it was decent for the price and worked with my HE-400, X1 and HD-650 back then. I didn't get to hear the HE-400S with my M/M stack, only heard the HE-400S with my friends high end equipment (Liquid Gold and AudioGD Master 7) and from my Fiio X3, between these two extremes there was not much difference so I don't believe the M/M stack would have a large effect on the 400S, or as you noted that since the HE-400S is easy to drive the value proposition is diminished.
I think EQ might be a better solution if you wanted to tune the sound signature of the 400S.
I have a Modi2uber but passed on the Magni2uber since I have better amps. My suggestion for a DAC/amp in this $300-400 range would be the Teac UD-301 that is on MassDrop for $349, to me its a better DAC than the Modi2uber and the headphone amp section is decent, probably close to the Magni. I've been thinking of getting a second one for my bedroom since it runs cool and I don't have to hold it down every time I plug or un-plug a headphone, unlike the Magni.
Since you mentioned channel imbalance, I think the UD-301 would be better since the volume pot is not linear and most of the time its around 12-1 location, well above any problems of channel imbalance but the Magni2uber has a gain switch so that might help also.