I pulled out the AC units from the windows and have put them back in the original boxes that they came in. Can I stack them one on top of another for storage? I know not to stack the units normally, but since they are in the manufacturer packaging I think it should be fine.
If you have put the units back in the original packing boxes they came in, then it should be fine to stack them. Normally, product boxes will indicate somewhere how high they can be stacked. That information is used by the people at the store and the people packing them on pallets. I would suspect that AC units could be stacked at least 3 high but do look on your boxes for that information.
I don’t think there's much of a problem putting the units into storage since they're already in boxes, but do take the extra precaution to make sure that they are padded properly, especially if you're storing them for a long time. Cardboard boxes are just so susceptible to damage and you don't want those units tumbling down all over the place..