I'm pretty new at this, so I may have made some terrible mistakes. I also tend to try to balance aesthetics and character concept vs performance, so I don't expect ever to approach min/max perfection. But this is my current setup for a sci-captain Sarr Theln built to use transphasic torpedoes:
I plan to replace the Breen deflector with the Adapted MACO deflector, and then swap either the engine or shields over from Adapted MACO to Breen to preserve the double 25% damage set bonuses. And eventually I'll replace those green transphasic compressors with vulnerability locators.
I expect to replace the neutronium with one additional Breen console for the two-piece bonus.
I have six space doff slots, currently occupied by two projectile officers, plus (I forget the actual specializations here): chance to proc aftershock gravity well, chance to knock engines offline in gravity well, chance to reduce deflector ability cooldown, and chance to increase exotic damage with emergency to aux.
I run with aux power maxed, shield power high, and engine and weapon power middling. Have a single omni beam for subsystem targeting.
Oh, lastly, that epic launcher has a spread proc, not a high yield proc, but spread doesn't seem to be available in the planner.
Shared cooldowns ensure that only 2 of those forward torps will be firing and it will mostly likely be the two rapid reloads. The Breen clusters are powerful but bugged and only actually fire 50% of the time.
I have a "torpedo boat" myself but that is 2 torpedoes and 6 other weapons. The shared cooldown for torpedo weapons means that it will pretty much always be the case with projectile weapons that they won't be a primary weapon system.
My boat is an aux to batt build that uses the reduced boff cooldowns to rapidly trigger torpedo spread 3. So it's not so much a "boat" as it is a skill/weapon/boff/doff combo.
What I've read — and so far what I've seen in practice — is that three rapid reload transphasics will interfere with each other due to shared cooldowns, but two rapid reloads and one normal 10-sec cooldown transphasic will fire in pretty good rotation. (In fact, I've considered adding a third projectile doff because if I don't get a proc, I'll occasionally see the three fire in sequence and then sit quietly cooling down.)
Thanks for the tip on the cluster torps. They have definitely seemed unreliable. Perhaps I need to throw a regular torp and a manually-triggered mine dropper in back...or perhaps they'd be more reliable if manually fired?