I would not do Dark Universe first. It is not officially part of early entry, and never gets crazy queues.
Personally I would still do Nintendo. It should now be far more manageable as I assume a large chunk of EPA will go to Ministry. So very likely you can do all three rides during EPA, even if you are not front of the line at the gates.
As a side effect, Ministry should hopefully also get reduced wait times throughout the day because many will do it in the morning. The main reason why I would not do Ministry during EPA is because it is still decently unreliable and therefore could waste all your EPA if it goes down early.