I've already found some mk IV and V Commander level items from the level 14 and 15 missions. I think the Laurentian system fleet action is the best place for high level loot. You find tons of awesome crap there. It's a hard MFer without good people though.
I can't login to check right now of course but I think that's the one I got all my high level stuff from. Not 100% sure though.
Honestly I'm kind of disappointed in the level of quality between ranks. Mk III stuff is hardly much better thank Mk II it seems. Well for some items anyways. Torpedos or shields or ground weapons for example. Sometimes the difference is pretty big though like for impulse engines, they have a very noticable/tangible improvement.
Lord Thot , try hitting em from the sides , the klingon ships are paper thin if you dont take em head on .
Space combat is pretty welll balanced , almost "too" easy once you develop good piloting skills and conversely seems a little tough before you learn the ropes and develop some tactics
Overall thattd suggest its about right... keep trying new tactics and learn to balance shields (using the arrow keys helps a bunch)
miranda vs. multiple BoPs or Raptors are hard... Sometimes vs. a battleship can still be an issue. The Rescue the Researchers boss is less hard than before but still pretty hard (I would say it's barely soloable at Level 7). Negh'vars are much easier than last CB playtest, they are easily soloable by level 4 or 5.
What really needs to be made more difficult is the ground combat. Even with 3 Boffs + random redshirt and very few groundskills trained (Boffs having level 3-4 groundskills, player char has level 1-2 groundskills) you can totally overkill the entire Gorn population on Kassae IV without dying a single time. You can dump all your skill points into space-skills and still pwn at ground combat, which is sort of unbalanced, by definiition...