I know Transphasic Torps are not that great, but I want to try anyway. I'm at Commander level at the moment so I cannot try them yet, but last night I had a go with a fore Plasma torpedo and aft Breen Cluster torpedo. It was difficult. Sometimes the high yield plasma torp and the cluster torp seemed to get shot down even before it left my ship. I will practice a bit more.
I also want to put the Abosolute Zero set on my ship instead of the usual Borg / Aegis stuff. That will help with the transphasics too.
I've done this. Not with a science ship, but with a fleet escort and it was long before the Breen purples were added to the Breen FE, so I may have to give this another shot.
Definitely go with the Breen Set and Rapid-Fire Transphasics. Since you're in a science ship you'll need that reduced cool down to keep continuous fire. Also get the best transphasic compressors you can get your hands on. You'll be at a slight disadvantage due to the DSSV having less Tac console slots.
You may want to go with only 2 torps up front, that way you can have a single beam for Target Subsystems. You don't need high power to debuff, so that'll give you one way to reduce/drop shields.
Tachyon Beam might be useful, but you'll probably want two copies of it. Charged Particle Burst is another good shield stripper; PBAE with 3k radius.
Honestly torpedo boats are kinda gimpy at this point in the game. They're not all that great in PvE because NPCs relative hull strength and shields are crazy compared to a player's (typically 5-10 times depending on mission difficulty).
In PvP they're OK, but again, transphasics aren't the way to go if you're planning on PvPing.