Baz, Cy and a few others updated a lot if not most of original game models for the Maelstrom Mod. I've included list below. But there were a few we never got round to, including the Sunbuster and Cardassian Outpost.
* CG Sovereign replaced stock USS Sovereign and Enterprise
* Wiley's Venture Refit Class Galaxy replaced stock USS Dauntless and Venture
* Wiley's new Akira replaced stock Akiras (Geronimo, Devore)
* Wiley's Nebula replaced stock Nebulas (Berkeley, Prometheus)
* Baz new Spacedock replaced stock FedStarbase
* Baz new Merchantman replaced Cardassian Karoon
* Baz new Cardassian and Kessok ships replaced stock
* Baz new SpaceFacility and FedOutpost replaced stock
* Baz Excelsior Refit as USS Khitomer (stock Nebula)
* Baz Bird Of Prey replaced stock
* Baz SFSY Freighter replaced stock
* DJ Curtis Orion replaced USS San Francisco (stock Galaxy)
* DJ Ambassador Refit replaced USS Zhukov (stock Ambassador)
* LC DDeridex replaced stock Warbird
* New Ferengi Marauder replaced stock
* cinqnic's Olympic Class replaced USS Nightingale (stock Nebula)
* Phoenix new Vorcha replaced stock (Jonka)
* Cy's new Transport replaced stock
* Cy's new CommArray/Satellite replaced stock
* Kophjaeger's Cardassian shipyard replaced stock Cardassian Station