Well D'kyr's hull is actually high for a Science Ship so I don't think that needs a buff (the only UFP sci ships that beat it are the Ft. Deep Space and the Nebula). Not sure about shields, maybe a modifier increase of .1.
For a universal BOFF slot it should be an Ensign, otherwise the ship becomes a copy of the Fleet Nebula if its Lt. or the Orb Weaver if Lt. Commander.
An extra Eng console seems like a good idea. Sci would also work but for sure it should not be Tactical.
My Romulan Liberated Borg character made it to Level 30 and beat the (old) Defense of New Romulus with the skill point bug.