Heavy Plasma Torpedoes are insanely tough to deal with sometimes. Here's my suggestions:
1. Make sure your power settings are set for Combat. (If they're on anything else, beam and cannon weapons are much much less effective) It may sound like a "Duh!" suggestion, but I've forgotten to make the changeover many times.
2. I recommend having more beam weapons on your ship, Beam Fire at Will can be extremely useful in dispatching the Heavy Plasma Torpedoes, if you time it right. The More beam weapons you can fire, the greater the chance that you'll knock them all out before they reach your ship.
3. Keep the ship moving, if a Warbird gets you in a tractor beam, your job gets much harder. I didn't see any Polarize Hull options in your Bridge Officers abilities. I'd add that on.
4. With heavy ships like the Romulan Warbird or a Battleship, sometimes you don't want to use your abilities immediately, in case they use theirs on you and it's a wash.
Hope that was somewhat helpful, Good Hunting.