Just to let you know all finally went well with the upgrade/migration from J2.5.9 to J3.0.3 after I uninstalled all possible non-CB/GJ plugins that might need a J3 specific version.
In case it helps anyone: (always backup first!)
Uninstall anything that might be incompatible or needs specific J3 installs, for me specifically it was:
Uninstall JSN PowerAdmin (they have a specific J3 version but on testing after J3 update that didn't work for me)
Uninstall All NoNumber extensions (including manually deleting the folder administrator/components/nonumberinstaller) (a big folder, 6MB, took a while via ftp)
Update:
UddeIM to latest (3.0) as per instructions (plus premium plugins)
Kunenea 3.0 Beta (just regular install over existing - worked fine but I don't have a large active forum yet, just a few test posts)
Complete CB/GJ install via Packager (with everything selected)
Ensure anything else is updated or removed if maybe it's not suitable for J3. For me I have a few RocketTheme extensions installed, these seemed to be fine but update to latest versions first. I did read of some people having problems if RokBox was published at install time, for good measure I deactivated its three parts and then reactivated after J3.0.3 update was done)
Finally using Components/Joomla updates and switching Options to STS release which then makes the J3.0.3 update show, just let it go to work, cross fingers and viola. It worked for me.
Lastly, backup, backup, backup! I did before, during and after. Saves a lot of time/pain if anything goes wrong.