Now I know that all of my issues were after installing the update and being able to log in (XMB freezes, crashes, What's New and PS Store broken etc) but I think that they may have been down to a corrupted user profile rather than the whole PS4 in my case. After Support went to initialising the console as their second option I decided to try and save 8 months of game installs by backing up my game saves then deactivating and deleting my user profile via another user on my PS4 (a user never affected by my issues). I then recreated my user, reactivated the PS4 and re-downloaded all of my game saves.
4 PS4 restarts later and it's still working fine. I've lost no data, there are no freezes or stuttering and all of the previously broken things work fine. I know a lot of people can't even install the update, but if you are having issues after actually installing it, this may be a last ditch effort to try before jumping straight into initialising the console.