Wordpress + Softaculous issues

My site has been through various iterations and themes over the years, in the last month or so I have been tidying it up focussing on getting certain Google Page Speeds up and removing plugins that are slowing page loads down.

However, the situation currently is as follows:

+ Some plugins will not deactivate or uninstall

This means I have hit a wall regards 'fixing' page speed. I am using the plugin Query Monitor to identify issues. So, for instance, with another plugin HIDEMYWP, I get php errors, it cannot find files.

I contacted my hosting company, Krystal, who said :

"That is because Softacalous cannot locate the install files for the primary domain, checking the public_html that does appear to be there but the file structure is a little scattered."

What I DON'T want is just a deletion of these directories, what I DO want is a fixing of the cause, to make my site, Softaculous, and me, happy again.

Krystal Support also added the following:
"One thing you could try is spawning up a temporary and blank WordPress installation, then use a WordPress migration plugin to export the current website to it.

Once done, if that imports as expected you could move it to replace the installation in public_html and simply update the database and site_URL so it functions on the primary domain."

Obviously, over to you and your expertise on how best to go about sorting everything out.

I'm keen to get this sorted!
Best
Chris