Discovered something else. For those sites that were "broken" after the upgrade I found the following worked, but this would be impossible to do if there were hundreds of sites. If I take the individual site form the sub space, cut and paste into sites, access the site in Share as the non-admin user with permissions, cut and paste the site back into the previous sub space, the site is no longer broken in Share for the non-admin user. Not sure what this means, only to be careful with upgrades.
UPDATE: Discovered that if I restart Tomcat all the references once again are gone. I can only conclude at this point for the Community edition there is not a safe upgrade path? But since this is a community edition and I'm in test mode I can live with this until I can get a better handle as to what is occurring and figure it out. Alfresco is a nice product.