Hi Peter and welcome to Support Forum.
I've just downloaded and installed AmiKit 9 (it's been long time!) and it worked for me on my macOS 10.14.6. Hope I can help you to make it work on yours too.
Launch AmiKit emulation, then select "OS3.9 CD" button. Now pres fn+F12 and in WinUAE go to "CD & Hard drives" section. At the bottom, click "Select image file" button. A window will open where you can select the location of your image. Now click "My computer", select Z: drive, then "Users" > "YourProfileName" > yourOS39.iso
After you double-click your OS39.iso file, the window will close and you get back to WinUAE. Now you should see a path to your ISO there. In my case it looks like this:Z:\Users\jan\OS\AmigaOS 3.9.iso
Now click OK to get back to the emulation and the CD should be recognised. At least it was here.
You can also check Quick Guide for the latest AmiKit XE. The Mac installation process, except the OS3.1.4 part, is the same: https://bit.ly/AmiKit-QuickGuide
Please let me know how it went for you.
PS: Regarding the CrystalUSB, please note it does not boot on Mac.