Hi Rene,
DB stuff
Delete from mp_modulesettings where moduleid NOT IN (SELECT moduleid from mp_modules);
Delete from mp_modulesettings where moduleid IN (SELECT moduleid from mp_modules WHERE moduledefid NOT IN (SELECT moduledefid FROM mp_moduledefinitions));
Hopefully there are no orphans but that will get rid of them if there are.
Don't worry about guid columns for now they are probably/hopefully ok.
Skins
I would copy the content from /Data/skins into /Data/Sites/[SiteID]/skins for both of your sites.
If css problem continues, view the source of the page and get the full url for the css ...csshandler.ashx?... and paste it into the browser and see if you get css or an error. If an error, you may be able to workaround by setting <add key="CombineCSS" value="false"/> in Web.config.
Encoding Problem
I forgot about this but, back in the day we were encoding the content going into the db and decoding it on the way out which was a mistaken design. So now we do not encode it and we do not decode it so any content that is already in there encoded needs to be decoded in the db. There is a utility page to assist with this. If you log in as admin and navigate to /Admin/dbUtils.aspx you will see it.
Hope it helps,
Joe