How can I bulk-change the folder permissions on macOS?

chmod has an -R option to apply changes recursively to a whole directory tree but I strongly recommend to not use it for your scenario as you can break quite a lot of things by applying it in places where you shouldn't.

Instead

• Log into your Mac as an administrative user and rerun JDisk. Not sure it will solve all your issues though as the tool seems to be cross-plattform and may not be aware of access right handling on macOS
• Check out the answers in How can I figure out what's slowly eating my HD space? for other tools

I would recommend OmniDiskSweeper or DaisyDisk as native Mac tools that can sort the entire volume by size, showing you what's using the space (and even delete it from within the app).

Apart from large application support files like sample libraries for Garageband, Logic, etc; then content in the User domain is likely to be the only thing that you can safely delete (and also the stuff that's taking up all the space).