<link rel="stylesheet" href="/css/combined.css">
You should run your combined js and css through a ...
Yes, it will affect it. Anything that comes after "hidden" will be weighted less, so you wanna avoid having keyword heavy stuff after "hidden".
This happens because of Auto Ads inserted by Adsense, the script in the core of the website allows AdSense to place ads wherever they want. I think you should also contact your web host if they do provide live chat to find out if they allow parsing of code or not, because some web host block it due to malicious activity.
Typically when replacing a Joomla website, I move all the files and folders in the root folder (e.g. /public_html) into a sub folder such as /public_html/old which I retain for a few weeks in case I need to retrieve anything I have forgotten about or need to compare the new website to the old website.
If it exists, you should probably leave the /.well-known ...
several folder/files that belong to Joomla
Do you mean only core files? Or files, which are important fo ruser, like images or pdf?
If you mean only Joomla core or extension files - they may be deleted. But if there are images or documents, which could be important for visitors - try to redirect them, or you will experience a kind of downgrade after switch....
If you are not using Joomla at all, my suggested step is to make a complete backup of the joomla site, then delete it and replace it with your files.
If you aren't using Joomla any more then you don't need any of the Joomla core files.
Watch out that you don't delete images or other assets that you may have uploaded and need in the new site.