Firstly, you won't be able to simply copy over the files in the .gconf directory, while your user is logged in on, as the running instance will take precedence, and changing the files out from under the process will have no effect.
And Shotwell uses dconf to store its settings now, so you'll likely need to export them from the one installation, and then import them in the new installation. I don't know if Shotwell itself has any export/import feature for backing up and restoring settings, but some applications do.
To export/import from/to gconf while it is running, you can use the
gconftool command line utility with it's --dump and --load options. Unfortunately, it seems the
gsettings command does not have similar options.