I am also running the refit, and this is what I run. At Captain level, there really isn't much you can put there. Depending on your Boff abilities, you can always put another Halon Console, or the Console that gives +18 to Deflector Field. That will increase your TSS. If it was me, I would either leave it empty(If you only do PvE), or put in another Halon Console if you PvP.
1 EPS flow regulator (Currently testing replacing this with an RCS regulator, because it improves my turn rate by 5 degrees, and I don't need an EPS flow regulator as much since I don't use Beam Overload)
1 Nutronium Alloy (Essential if you PvP, I never leave ESD without it, and don't think any ship should)
Borg Universal console
1 Halon System
4 Prefire Chamber
THY 1, CRF 1, THY 3, CRF 2, TT 1, TT1, APB 1, & APO 3. (The reason for this, is when you first strike, hit APO, APA, CRF 2, THY 3, & TT 1. This sends CRF 1, THY 1, APB 1, and TT 1 in a 15 second cool-down. Just keep switching between the two.
EPtS 1 & 2 (Not only do they raise your shields, but they give you shield resistance, and shield power which is great for the Borg shields)
Polarized Hull 1
Hazard Emitters 2
These share a cool down. But if you time it right, it doesn't matter. Polarized Hull only lasts for 15 seconds. That is how long it sends HE into a cool down. So you hit Polarized hull, then HE 15 seconds later.
This is what you do:
Cloak, get behind someone. Hit all your abilities. Fire on my mark, APO, APA, CRF 2, THY 3, & TT 1.
Decloak. and fire.