ok just brain storming here what if you were to "Copy" the cells and then clear them out? scripts, npcs, game markers, etc etc, then as far at the supply lines you could make a settlement at CIT with a workshop that was linked to the workshop of the interior of the institute. like build your own vault, and basement living did. but if you did the new cells with the clean out then have the teleports switched via script/quest that way you wouldn't be touching the actual institute. and maybe a lot less problems.