Hi I thought I had resolved the issue of my site dashboard not being available after my upgrade from 3.4d to 4.2c by resetting the preset using a JS Webscript. Unfortunately this fix is lost each time Tomcat is restarted.
Solved the issue by doing the upgrade again, but this time I made the modifications to the permissionDefinitions.xml and SitePermissionDeffinitions.xml on the 4.0e leg of the upgrade to reflect the changes made on the 3.4d version and I can now access my site dashboard.