For a guide, a sheet of mylar or polyethylene or polypropylene wrapped into a cylinder around the rotor would work just fine.
... but then you have to remove it after assembling at least one of the end bells. It may or may not be reusable after extraction.
Maybe some perforated sheet could be stretched over the rotor and left in place, to be shredded on first start. With my luck, the remains would get balled up and do major damage within the warranty period, but maybe you can do better. Maybe a mesh tube, e.g. from Caplugs, could be made thin enough to remove or frangible enough to leave and shred, or soluble in something you could immerse the assembly in, e.g. PVA and alcohol.
If the tolerance stack from stator ID to shell is looser than the air gap, maybe a rigid fixture won't work. I hesitate to recommend something like a self-adjusting rigid fixture, e.g. a robot that uses a laser or a probe to locate the stator ID, then guides the rotor along its axis, well, it can be done, but that kind of stuff gets expensive fast.
Mike Halloran
Pembroke Pines, FL, USA