MJ, Steam and Transformer Upgrades are the only things I would allow to the Matter Fabricator. In case of Transformer Upgrades I would ofcourse nerf the maximum Input Voltage of the Matter Fabricator.
How about making Transformer upgrades increase maximum EU/t input?
Like : 8192 (0) , 16384 (1) , 24576 (2) , 32768 (3), 40960 (4)
If you think it is too cheap you can make a new upgrade : MatterFab Input Upgrade, requires three overclocker, three HV transformer upgrade, 1 highly advanced machine block and 2 energy flow circuits.
A small request : can you add a Lapotronic Nano Chestplate which is just a combination of nano chestplate and lapotron pack, which has both nano chestplate armor and lapotron energy storage.
It would be useful so you won't lack chest armor when you have a lapotron pack.
Maybe it has only 5kk EU as a nerf to the storage as to fit both together some storage had to be cut off.