Dykstra is responsible for the opening klingon, the epsilon 9 stuff, a lot of viewscreen graphics, torpedoes and the EXTERIOR of the physical vger, including the first maw that opens up at the front end. He also got stuck with the terrible officer's lounge mess, where production in its infinite wisdom -- how wise & co didn't realize this ahead of time I can't imagine -- shot blue-grey uniforms against a bluescreen.
Trumbull had the cloud (the super pretty stuff), all of the vger interiors (including the terrible wingwalk stuff, which in the theater was only really bad in the profile shot of the saucer, the one where the ship seems about the size of a barn ... the first shot where they come up on the lift, while awful on DVD and not great on laser, seemed fine in the theater.) And he had 98% of the Ent shots (Dykstra did a couple super long shots with a tiny E-A) and the travel pod and drydock and orbital station.
Trumbull's people handled San Francisco and Vulcan, but don't blame them for the Vulcan establishing shots - somebody (katz?) pulled those and gave them to some other company to do, which is why they absolutely suck compared to the version there are many images of Matthew Yuricich painting. That's info from TGT, but I believe it completely. Rocco Gioffre might know more about all this, he was MY's apprentice, and he posts at the stopmotionanimation.com forum for matte paintings (or he did before they redesigned it, haven't been there in awhile.)
That's off the top of my head, I'm sure I'm missing tons of stuff, there are something like 560 VFX shots in the movie.
edit addon: as for why paramount didn't take back and preserve all of the effective elements ... well, that's just brain-dead to me, as in a no-brainer that they still screwed up. Then again, look at how they treated the quarter-million dollar drydock ... it got stuck in some storage facility for nearly 15 years and wasn't protected when shipped, so it was pretty much debris suspended by its internal wiring by the time ILM got it for GENERATIONS.