I like the shipyard method, in this case a retrofit frame is built to the stations new dimensions or greater, link to retrofit computer, load the retrofit design, make sure there's enough storage space and material linked to the retrofit controller, then hit the retrofit button.
When the retrofit design is loaded it shows the shipyard like projection of the stations new layout with the ability to rotate and shift its final position, as long as it fits within the retrofit frame. When adjustments are finalized a list of needed materials is then calculated and displayed within the appropriate menu in the retrofit controller, taking into account the blocks of the existing structure.
Would be great if warp gate and wireless links could be maintained through the process as well.
Might want it to give out a warning if there is a player shop on the structure with credits and materials still in it.