Remember that starship combat is abstracted in STA. The game doesn’t care if you have the Oberth’s singular phaser bank or the ten of a Galaxy Class. The single photon Torpedo launcher of a constitution class or the glibbidybabillion of an Akira Class. The only thing that matters is that you have them or not. So give an Oberth the upgrade with the Quantum Torpedos they now have access to quantum torpedos, in addition to any other (none) torpedoes they already have.
That’s how I read it anyway.
I’ll give you that 
I’m a strong supporter of the abstract nature of the system, but I was quibbling over the wording… To me the talent implies the addition of the ammunition not the system… By default, the Oberth has no torpedoes so would be unlikely to have the requisite launcher and targetting systems.
All of which is minor and not really on topic so I’ll shut up!
It’s testing “an experimental engine system designed to exceed warp 5 without damaging subspace.”
What I did to my group they are senior officers of the USS Akira which I’m taking through the Dominion war years. My Episode 2 I converted a old FASA star trek module Lost and Presumed Dead. The USS Akira detected a Federation Distress call on the old Cochran Subspace band which hasn’t been used in 115 years its from the USS Victory NCC-1760 a constitution class cruiser. Yes I changed the name from the Republic to Victory to line up with DS-9 series. You could do something similar but dump the whole mess in the junior officers lap.
The adventure Entropy’s Demise has one at the end.
A while back I took my group through it albeit heavily modified to fit our campaign. The adventure calls for the U.S.S. Hamilton to have travelled through time but I’m not a fan of the amount of time travel in trek so I had the ship cross dimensions and when it returned to our universe the entire crew was found dead with it the “Dragon” from Space 1999 lurking in the engine room in addition what was written.
There’s an adventure in the FASA Star Trek III sourcebook update about a missing federation ship, might be worth a look.
If you count a starship with a deceased crew as an abandoned vessel, “Ghosts of Conscience”–one of the three scenarios included with the original FASA edition of Star Trek–is not a bad one to use and should be easy to adapt to Mōdiphiüs’ system.
The first adventure in the These Are the Voyages 1 book deals with salvaging a NX class ship caught in a temporal anomaly. It’s not abandoned, but the crew isn’t really in shape psychologically to bring it home, so it can be up to the PCs to do it.