Na not too bad. You sort it all like this:
- make tool that displays information you need to decide category of material.
- make UMG buttons that are connected to classes/types of material displayed
- you press button, decide type of material, apply physical mat, rename it (move to new folder), and save. Even saving in folder for category, can let you apply material in second pass.
- going trough 1000 mats this way should take 1-2 hours, and bonus is you have all nicely sorted.