It turns out your STL file is not clean. There are many duplicate vertices/triangles. Please see attached. My recommendation is you start with much simpler models to get familiar with the procedure. See 3. Tutorials — MFiX 21.3 documentation for some examples. For non-rectangular geometries, the cut-cell method is the only option. To clean your STL file, use the CAD sofware you used to generate the file, it should have options to remove duplicates and recompute normals.
What worries me in your simulation is that the inlet velocity is quite high (around 9 m/s) for the size of the inlet tube (around 2.5 mm), and you have many other tubes smaller than 1 mm, so you will end up with very large velocities that require tiny time steps (see picture below). In the attached, I used a grid spacing that will get you the bare minimum to resolve the internal tubes, and I had to use fairly large values of the snap and small cell tolerances to get it to run (you may be able to find a better combination that work too). I also removed duplicates in the stl file, which went from 2894 triangles to 1298. It still has many stretched triangles, and you need to set a facet angle tolerance to zero or close to zero so no facet is excluded. You want to see this
Total number of facets read = 1298
Number of valid facets = 1298
Number of ignored facets = 0
If you have ignored facets, this will create holes in the stl and the meshing will likely fail.
chamber_delicate_structure2_clean.mfx (15.3 KB)
chamber_delicate_structure2_clean.STL (63.5 KB)