IPhone – How to i get itunes to backup the iphone with limited disk. I linked the backup dir to an ext drive with space yet still won’t backup

There is an application called iPhone Backup Extractor that will help you extract data from an iPhone backup. it will convert the files you see in the backup with randomly generated names to things you will recognise.

When you run the application and identify the backup you want it to use it'll give you a list of all the application data contained within the backup. BTW you'll need to move the backup folder so its sitting at /Users/YOURUSERNAME/Library/Application Support/MobileSync/Backup/LONG_GIBBERISH_STRING for iPhone Backup Extractor to find it.

I'm not 100% certain where Apple stores books/documents that haven't been purchased but my guess would be within either "com.apple.iBooks" or "iOS Files".

It's likely in /Volumes/MobileBackups and you can easily delete it by entering Time Machine and navigating to the folder where the file existed. Select the file then command-click (right-click) and delete all backups of that file.

Normally, the system information window shows the backup space, but I have seen this window get hung up and not properly report storage space when Spotlight and/or the disk catalog are wonky.

You can also wipe all local backups by disabling the local store:

 sudo tmutil disablelocal

If the above steps doesn't work, you'll want to boot into recovery mode and run Disk Utility to check that the directory structure and file system catalog are correct. A fsck -fy / in single user mode is also equivalent if you are so inclined to fix things from terminal or want to perform a safe boot and have the system clean things up systematically.