Just found this topic and have a similar Query;
I “have” to do a 2 by 2 stacking for my NDX 2, 252, 250 DR and Supercap.
From above I deduct to do it like this (as well as using the space I have and aesthetics).
Headline
Nac252 # 250DR
NDX -2 # Supercap
The # represents a wooden plank 
Any suggestions?
The order looks about right to me, although I have no experience of the headline. Not sure what the wooden plank is, are you putting the boxes on shelves or a rack, not directly on top of each other?
Put the Headline between the 252 and NDX as it will give more space around the 252 resulting in better sound.
If you can, have a blank space between the 250 and Supercap. You need 3 shelves anyway on the brains side. If you have a PS for the Headline that can always go on this shelf.
My cupboard is such that the equipment is directly on top of each other. The wooden plank is the divider. in the cupboard. So the headline cannot in between.
Everyone is going to tell you that such high end kit should not be stacked on top of each other and that will not do the kit justice to use it like that. I’m not sure how true that really is just that is what people will say.
Could you add additional shelves to your cupboard?
No space… but will think about it, redo the cuboard 
My train of thought is that the pieces it self are cage of Faraday (blocking all electronic interference), so I only have to worry about heat…
Is my train just derailing?
Is it possible to put the two shelves of the fraim on the side, which can give you 2 fraims? in that matter you should be able to separate the ps from the amp, pre, and nds. It really uplifted the sound for me.
I will have to redo my cupboard. Will give it a thought, and may even change whole set up (Also read al the FAQ)
I do not fully understand the rational behind the stacking (and do not discard a audible difference either).
What is the reasoning/science behind the stacking?
Very very simply to keep the interference of different units to a minimum. If everything is isolated and spaced at optimin distances not forgetting correct cable dressing then the sound difference should certainly be audible. You have decent kit and it seems a shame not to set it up ‘correctly’ not withstanding various room/lifestyle issues that we all have.
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