I spend the better part of a day fixing problems with the site. Cleaning up database managed to get the site working better. Now the permalinks work as expected so the rendering of the site is substantially improved. I also noted that image problems are fixed after running the bulk image regenerate tool.
Issues with Apache vhost and CERTBOT had to be mastered to be able to get the site operational.
New problems with JetPack are a minor problem, the site can made so with alternatives. Due to commercial nature the intentional crippling of functions does limit the capabilities substantially.
Cleaning up the database, Yoast SEO had created several tables that doubled the database size. This is very bad design and small wonder it’s not widely used. This package also is crippled with a subscription demanded.