Manually restoring macOS System folder I have been trying to restore using migration assistant from an Airport Time Capsule with no success despite following multiple support avenues.

I’m now trying to manually restore all my files but the issue I have encountered is that even using the root account there are certain files that I cannot remove and replace with the files from the backup.

In particular I’m trying to ‘swap out’ the /Macintosh HD/System/ folder. Any ideas appreciated.
I am not sure how you are restoring from backup but you can't replace active system files, nor would you want to.

The preferred way to restore a Mac would be to install/reinstall the operating system from whatever source you have. Once that is done use your Time Machine backup to then restore your files, applications and system settings.

The latter would be those files that the system would change to reflect preferences, settings and other changes you have made to macOS. Some of which may be located inside the System folder(s).