Compounding surface parts is tricky - you need perfect alignments and proper partitions: Orthogonal shell mesh model
Especially see this: Contact Generations issue Shell_Solid - #16 by Matej
For example, you may need to split this khaki face here:
It’s usually easier to do the whole thing in CAD software. You could try the Fuzzy boolean union followed by Part → Convert to Solid approach in FreeCAD as mentioned above.
But even if you can’t merge some parts, tie constraints are always an option. However, they can be problematic for shell edges: Tie constraint on the edges of 2D elements - Analysis issues - CalculiX (official versions are on www.calculix.de, the official GitHub repository is at https://github.com/Dhondtguido/CalculiX). (then you could try e.g. tied contact).
Also, keep in mind that the Thicken Shell Mesh tool operates on whole parts, so you would need to import the regions where you want to apply it separately. But you only need the solid segments for rigid body constraint if you plan to include Nlgeom or use ccx 2.23.
