I went back to Twenty Fifteen theme with all the plugins deactivated. I have also done diffs for the plugins with the master versions and found no differences.
All I can think of is that Wordfence Security of Simple Firewall have made changes to system files (outside of plugins and the theme) to improve security but to break Connections. i.e. if those plugins are deactivated I’m assuming they can still make changes in other places? I’m not sure. I just can’t think of what else it could be.
I feel the only way forward now is to create a blank WordPress installation on the same host, and slowly add everything back in, one step at a time. i.e. install a plugin. Copy one setting across at a time, while testing for the issue. Then put each page and post back one at a time. It is hugely laborious but I don’t see another way to track this down. I can eventually then do a recursive diff between all the files to see if it was a file issue, if all the files are functionally the same then it would mean the database had become corrupted somehow.