So far, it seems that the problem lurks somewhere in the <configs> part of the domain.xml.
I have moved the <resources> part from the upgraded domain.xml into the original GF V3 domain.xml and both the admin gui and my app worked as intenden.
Maybe you can also try this approach to see if this fixes the problem for you as well and if we are very lucky someone at Oracle cares about fixing asupgrade / domain upgrade.
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