Hello,
1. What did you do to disable the stock status? I just tested an added a variable download product, using three attributes. I entered the stock. The product saved and was bale to be added to my cart without issue. All attributes saved the info I input.
2. This was not an issue for me when creating a variable download. I selected the attributes, clicked the variations tab, selected “Create Variations from all attributes” and then filled in the info for each variation.
3. Categories are added by the admin. wp admin > products > categories.