Hi,
it is not easy to have a perfect solution of your problem. First you are far from the origin and Rhino doesn’t like it for mesh as most of the time mesh is using float representation. Now there is a double precision mesh vertex in Rhino 6 but I am not sure it is well implemented everywhere.
It could be good also so separate the differents groups ou metaballs.
For each group make the slices in 3 planes cf. Metaballs, the naughty way. - Grasshopper …
You could use Dendro that is very good. Dendro is based on OpenVdb and is quite robust.
I applied David’s Method, so I generate planes in the 3 directions (beware geometry is here centered on zero)
Then extract the points (you have to play with Metaballs accuracy and Rhino Tolerances)
Then bake them in Rhinoceros
Then apply the MeshFromPoints command for each group of points.
metaballs LD.gh (34.1 KB)
A version with geometry not necesseraly centered
metaballs LD.gh (34.1 KB)