Circuitry: Dont have to say much about that, as it's too vague.
But please consider coding the machine so you are able to auto-craft circuits somehow (like the rp project table, but pull-able?)
Machine rework: (i have to say this are just idea that came into my head when reading this, some of them are probably not even possible)
First off i though about multi-block cooling systems -which you would need to extremely powerfull machines, but then you have the space problem, and that doesnt look nice for workshops and is only feasable for factories.
It would be nice to have a grid to put different modules/circuits the machine in.
Really bad image: click me
The different colored squares are the different sides of the block (each side has 5 access-points)
You could craft youself different modules (f.e. 'Heatpipe','Lv-Input','Mv-Input','Output Module','Input Module') and connect a cooling system(block) to one side, the Eu input to another, a storage chest or rp relay to yet another side for automatic output when the output slot is full.
You would be able to click onto an empty field for it to create a pre-set element (Proccessing Unit, Storage(you could chain storage modules before the actual storage) and so on). You would probably need some cables, 'tubes' or so for stuff to flow in.
You would only have to recalculate the configuration when there are changes made to the config...
Yea i know.. it isnt that thought out/practical, but as you're on it, maybe it gives you a better idea.
don
Smog:
Yay.
'Smog controllers' - wouldn't it be a good idea to just call the block controller and use it for storing all kinds of information? I don't know what you would store in there at the moment, but it sure could be usefull!
Smog should spread relatively fast, not like taint in thaumcraft.. You can have a few chunks next to eachother full of taint, clean one out and the other ones won't even notice.
It should be too hard/resource intensive to calculate where the next controller is located if you use even placements (f.e. one block every 4 chunks on chunk 4 coords x0,z0) and that shouldn't make distributing smog very hard.
You also need to think about 'cheater' who will break their controller (or do that on accident...)
Airtight rooms: When there is no space left for smog, the machines buffer should start filling up & causing damage too the machine, that would prevent just ignoring the fact you can't access the machine by normal means anymore.
Project V:
Noooo, i need to know! :<