Does your warp core have combat benefits on it? Im not sure of the attribute flags (Wish it was spelled out on academy).
Your ship is NOT a T5U on Academy, did cryptic give you a T5U upgrade token? The extra console is very useful.
The THIRD set power of MACO Space (Heavy Graviton Beam) seems a rather useless skill. 3k kinetic dmg every 2 minutes is not worth it. So I would actually look into benefits of other 2-set bonuses (OR) fleet items and consider dropping the Engine or Deflector.
I would put the Zero Point module in an engineering or sci slot. Maybe the Delta set (gel pack and proton beam) aren't helping you as much as you would otherwise hope? the third set bonus that has looks interesting, but without it, I think they are doing you more harm than good.
With the above suggestions, my biggest recommendation is to use antiproton tactical consoles (and use as many as you can). When it comes to sacrafice in my opinion, the sci/eng consoles can take a hit.
And my favorite piece of advice I give everyone, cause, hey, it helps even a little:
http://sto.gamepedia.com/Subspace_Field_Modulator