The answer to issues 1 and 3 was obvious, I just wish Sparx Systems support tried to at least understand/read the change requests and OCS/WebEA had better error messages.
When we carried out the upgrade, we found that none of the database connections were working and, since it is not possible to edit the connection strings we had to recreate them all and, of course, when creating a model connection the "Enable Pro Features (OSLC, WebEA and Integration)" setting is disabled by default.
The 2nd issue is still a mystery to us.
One other point regarding database connections, the new "Native Connections" force PCS administrators to specify a username and password, instead of using the username, in our case Active Directory service account, running the PCS windows service. This is rather unfortunate and, in my opinion, unecessary.