The science vessel is mostly shields, once those are breached it goes down easily.
I have never used the avalanche, too much damage against smaller targets and only one shot against larger ones. I phased out most missiles for meteors, even though I have to pay 150k for each. I have an implosion launcher on my Devastator though.
I still have quite a few gauss cannons in the light slots, because I have so much ammo for them, and they are more than adequate for most targets, up until medium warships. They have trouble with the armor on heavier ones.
You could try the same setup again and use the menace class as a tank. Red Codex' ship has 2 heavy slots, which help as well, even if it is just 120mm cannons. But the other ones can tank as well.