my impression of the screenshots:
your expecting to much magic to happen from messy geometry.
your aim should be to have a single closed subd, polysurface or mesh.
approach 1: did you try to build your geometry with mulitpipe ?
approach 2A: with some coffeebreak shrinkwrap might generate a single watertight mesh.
approach 2B: use the initial center-curves to generate a pointcloud, divide them by distance, use the option inflate points/vertices and offset in shrinkwrap.
approach 3: implicit surfaces might do the the trick
my guess: 2B might do it.
kind regards - tom