I have been thinking about most of the items you mentioned, but have not definitely decided what to do with them.
There is a concept for expansion of the base, but I'm not sure whether I will implement it.
This special shell might be a special unit in combat or necessary for some important side mission, so don't lose it yet
Giving an under verse item to shady and triggering an alternative path to install them could be a way to go. Maybe she can sell your very expensive integrator tools, which are consumed upon installation.
Those would not ruin the latest quest so that could be an option