what changes?

Depends on how you're specced.

I only run a Bio-Neural Warhead. If it is part of the change, I'll be bummed. But, it's not necessarily what gets me the most kills.

So, I doubt my build is going to change much.

These from the release notes for 2/14/13:

Tricobalt Shockwave Torpedoes should no longer fire in a Spread pattern.
Updated Tricobalt Mines & Triciobalt Torpedoes:
Reduced the cooldown of both of these weapon types from 60sec to 30sec.
Their damage has been halved as a result of this cooldown reduction, keeping their Damage-per-Second constant.
The shared Cooldown on multiple Tricobalt Mines has been reduced from 30sec to 15sec.
The shared Cooldown on multiple Tricobalt Torpedoes has been reduced from 30sec to 15sec.
The global Cooldown for all Tricobalt devices has been reduced from 15sec to 5sec.

I run a 2 Tricobalt Mine setup. Have to try if this is still viable.

It'll still be relatively useful, but you won't be killing cubes with a single cloaked DPB3-buffed mine-drop flyby anymore.

You don't need 2xTT on a B'rel torp boat because it only needs 1 Cmdr or a Lt Cmdr Tac station, no more. Other boff stations should be for eng and sci abilities.

I go with this right now although I may drop DPB3 soon, not sure. It is a little heavy on heals, this lets it almost always survive long enough to cloak again when decloaked, and makes a good backup healer.

I keep another sci ability like scramble sensors trained on my boff that is in the Lt universal station and switch him around with the eng boff that is in my Lt Cmdr station sometimes to let me quickly switch abilities as needed.

Cmdr TT1, TS2, THY3, DPB3
Lt Cmdr- ET1, Aux2SIF1, EWP1
Lt -EPTS1 RSP1
Lt-PH1, HE2

My loadouts change a lot, sometimes Romulan, Omega, and 2 regular plasma torps up front, sometimes 3 transphasics and a cluster torp up front, and sometimes a quantum, harghpeng, Omega and Romulan. Usually I use 2 tricobalt mines in back, or 1 tricobalt and 1 plasma or 1 tricobalt and 1 transphasic mine depending on what torps im using.

All transphasic loadout works best for pvp other torps better in pve

Interesting setup.

Always nice to see what kind of torp setup the others run.

Actually I'm in with Quantum MkXII Borg, Rapid Transph., Bio-Neural and Harghpeng for PvE. Any other suggestions?

I should add that I have Omega on Tier 2 and Romulan on Tier 1

I never had much success with transphasic in pve, shields normally go down fast anyway so I hit harder with other torps. A regular plasma torp could be a better option then the transphasic for now, then upgrade it to Romulan when possible. If you also want to try the Omega torp I would only replace the Bio neural with it as you need most of your torps to fire fast and proc the torpedo doffs, and the Omega torp won't proc them anymore.

Your BOFF setup looks good. I think about using only one tac. BOFF, too. The only thing I would change is PH1 to JS1 as this is a good possibility to get off with tractors.

I don't use mines and I use two tactical BOFFs for buffing as many torpedo launches as I can.

I have no use for shield heals, since I'm rarely decloaked.

I had that same setup as you did up until a few days ago. I just upgraded my Bog Quantums to the Fleet Advanced Quantums. Higher damage, and the Borg proc is broken anyways (according to the devs).

On my aft, I use a Chroniton mk XII [crtd][crth]x2 and a Borg plasma. I just hit T4 reputation on my Klingon, so I'll be picking up the Omega torpedo in a few days to replace the Borg plasma.