The issues were related to partitioning, I ended up rebuilding the model to be a bit more simple (just single shell beams, not tubes) and cut it into 400 parts in CAD so that it would convert into a single part without errors. This works just fine and it runs in 90 seconds.
I have been talking with Matej and there will be automatic tie functionality before long, that would have greatly simplify this particular project. I was also able to mesh this in Netgen so that is another option.
There are many different ways to produce input files for the Calculix solver, at this moment I am using PerPoMax as it is a interesting project. I may change my mind but so far it is generally working just fine. I should test out some of the other options but would rather focus on solving problems than mess around with all the possible options.