I rethink things all the time as I read more science papers and journals.The AG you describe is perhaps a step on the way to full AG control (-ve and +ve). I my novel advanced battery tech and subatomic manipulation thieves this.
I now think that Anti-Gravity is the wrong term to use because it suggests the nullification or removal of gravity. What makes more sense is to over-power the effects of gravity. If anything, the device would be a gravity amplifier or something? If gravity on a surface is repulsed equally to the gravity working against it, the surface should float suspended. Increase or decrease that repulsion 'field?' to raise or lower the surface. Then its a simple matter of tractoring or pushing the object thru the air. However, the more mass there is the grater the force needed to start it moving and start it stopping.
With the right kind of nano-collector all matter would become 'fuel' to create different matter according to the 'fuel's' atomic structure.For the matter conversion you have to rearrange protons, neutrons and electrons (decay process) so just store the materials raw that are needed and process them when needed. Whatever way it's done you won't get rid of the problem of transporting mass if they are stored (in a Spaceship as in my case as on a long trip material may be few and far between).
A nano-contol AI would be needed and a set of nano-bots but anything could be raw materials.
With nano, its not splitting apart atoms, it is rearranging existing atoms into different molecular chains.
For example, it might use raw materials of carbon based molecules to create a carbon nanotube or bucky ball.
Technically, its not converting atoms its converting molecules.
^^^ATOM STRUCTURE^^^A carbon atom will still be a carbon atom and a lead atom will still be a lead atom, and so on.
An atom is stable or unstable according to the proton, neutron and electron balance.
Remove one part and the atom could become unstable.
Chances are, the conversion process would require removing multiple components of the atom at the same exact time. Then you would have to 'put' the removed components someplace safe so they don't collide with other nearby atoms.
To convert matter at the atomic level would require nuclear fusion and nuclear fission which gives off a lot of energy.
Converting molecules is much safer and a whole lot easier.
On your spaceship, you might have retractable collector 'sails' that collect matter floating in space as you need it, not really storing anything but the finished products. Plus, any object already on the ship, including the ship itself and its occupants could be raw materials.