I´m currently working on a Tool to get rid of a lot of problems mentioned here. Right now the Tool is able to batch rename files, remove duplicates and relink everything correctly, sort all assets in appropriate folders, set linear color space for mask textures such as occlusion/roughness/metallic. Here is a link to the current state https://youtu.be/GFZeC59GMgs
The delete all unused assets is next on my list. It´s really a headache. If you guys have any further wishes please let me know!
-Edit: Updated the tool, everything runs smoothly now. Find the tread here.