1) Any thoughts on the mechanics of making a construct or animated object large and strong enough to carry a ship,crew,and cargo? Plus it should fly. My plan is to use it as the core of the ship and build the ship around it.
2) Any thoughts on additional features like long range weapons or a sensor array? How would one do these things staying as close to RAW as possible?
Why not just animate the ship as a whole? Animated Ship is actually the listed Colossal Animated Object. You'd need Craft Construct or Animate Object & Permanency.
Cost of an Animated object is listed at Cost of Object + [(Animated Object's HD + CP) * 1000]. Halved cost if you craft it yourself.
Use "Additional Movement" to get Fly (Clumsy) for 1 construction point and you're sorted.
Looking at the Animated Object entry on d20pfsrd, it should have most of what you'd need to create what you're talking about. Pick your ship of choice in terms of size and then craft away.
You might run into difficulty having the Animated Object and ranged weapons, as ranged attacks for animated objects are pretty limited. But nothing stops you mounting ballistae/catapults or whatnot on top of it and relying on crew to fire them.