I never cared for the Daedalus in it's other form. It looked like the ball end would smash into the ass end when the ship went to warp. Way too fragile a design in my opinion.
The Azrael-class is the same ship of the Saladin. The Aquila is a name from a list of ships from the Hermes-class(not that kingdom from Conan the Barbarian); and the Clrak-class came from the Ptolemy-class ship of the same name. Columbus I figured was appropriate for my other ship, being mostly an explorer, although naming it after an early explorer that unintentionally misplace thousands of Native Americans and caused the cultural extinction of a few Central and South American civilizations might prove otherwise.
As for the Preservers I doubt they created the Doomsday Machine. Doesn't fit their description. However if they did create it, I assume they only did so to prevent other lifeforms to go extinct if it was in fact used to fight the Borg. I find it very unlikely that it was a weapon used against the Borg.