When I had similar graphics but quite different data problems, I made a work flow: construct and manipulate Graphics objects and Show them together, in my case with resized external photos, in Mathematica.
Each unit I exported as scalable PDF and 'placed' the pdfs in different layers into Adobe Ilustrator where they can be placed, resized and bound together to subunits.
Illustrator seems to be a reliabe basis for grouping, implanting, text writing, making projections to parts and layers and, printing what is seen on the screen, and never complains about too liitle memory. By the time used, the print process takes to translate a vector graphics into printer lines, one may get an impression, why an interpreting language cannot do such things.
Later trying import of the results to InkScape are of no use.
I tried your example, it simply does not work with tubes by time and memory.
