Okay I've been pretty busy so I'll just work on answering the straight questions first.
Storage: Generic stasis unit, available in any hospital unit. All it has to do is keep the nanomachines inert or on standby. Most sci-fi situations envision these to be cylindrical or cube like. Depends on the brand, make, and model.
Administration: Surgical, typically when the cybernetic implant is being installed. Due to the complexity of cybernetic components removal of wiring and circuitry in an already existing unit is more complicated than replacing it with a new one. The new component is 'hollowed out' and set for acceptance of the biological replacement. During the surgery the part is grafted and the biological supplement inserted. It grows along with the grafting process. The growth is accelerated and stabilized within a few hours of the surgery. Afterwards it heals along with regular recovery time typical of cybernetic surgery.
Laws: Normal laws and procedures according to regular cybernetics. Licensing not typical except for the facilities that perform the procedure in accordance to standard medical laws.
Creation: The biological component is generated via a template that is programmed into the nanomachinery. Adjustments are added after a sample is taken from the subject about to receive the cybernetic component. The medical trial period should be over if it is to be considered ready for public use. At least I would imagine that the trial phase would be over. I doubt it would serve any purpose IC to delay things for medical tests unless there's a story involved with it. And I think I could come up with something but mainly on the latter end when testing is done.
Saftey: Typical safeties used on most cybernetics apply. Emergency shut offs in case of power overload, pain mechanism disabling, safety overrides, etc. Usually determined by the type of component.
Transportation: Unformed and uncoded nanomachinery can be moved safely via storage modes mentioned above. Fully formed components cannot be removed without damaging the system unless performed in a surgical facility.
On to the Feedback portion.
EMP: The whole purpose for this design is to render EMP ineffective against cybernetics. Since EMP only affects the wiring and circuitry of cybernetics, having them replaced with the biological equivelent makes the components more surviveable. There is no need for shielding anything. Full conversion cyborgs especially have no need to be concerned and can lighten their loads substantially. Because the nanomachinery maintains the biological components there is no need for a biological body.
Synthetic Biological Material: Yes it makes sense that unless it was made out of something like plastic or rubber created to look like biological stuff it would be synthetic. Since this is real biological material being used then the name Artificially Cultured Biological Material is what it will be changed to when referring to the substance.
Regeneration: All your ideas make sense. That was actually close to what I was considering when it came to a control mechanism that would interface with the signals from the brain. However those would be mostly limbs. Cybernetic organs and systems like eyes and ears would not need the secondary brain. Other than the minor brain there would be no other example where the system could self-improve.
Advantages/Disadvantages: Existing neural technology in cybernetics has not been applied like this before. This is more a design concept than new technology. No one has ever put forth this idea before to attempt to solve the problem of EMP. The reduced weight and signature are bonuses. That was pretty much it.
Your suggested ideas while good had already been put forth by me but due to server shifts they kept getting lost. I put them forth as Skill Downloads that could be downloaded into the brain and learned. I guess I'll have to redo that article. Again. It will be some time though because just writing this up took me forever.