Dallas - nice work with the new boolean cylinders!
I've attached an adjusted .geo input (Assemb_v2.geo) that generates a mesh (44,897 tetrahedra) which PyFR should be able to load.
At the top of the file you can see I use variables {x1, x2, x3} to toggle a shorted barrel length (makes it easier to examine the mesh).
However, given the geometry, I'm not sure which region you intend to be the actual simulation ("fluid") domain... ?
Loading the attached .geo into gmsh and pressing [Mesh -> 3d], I see 5 small cylinders labeled "inlet1" : "inlet5" going from (x= -2 : x= 0) through the wide disk, as inlets into the long barrel chamber formed by your "inside wall" surface.
Question: do you want to model the structure generated by this geometry, or some volume enclosing this structure? i.e., do you want to simulate the inlet/pipe material, or some fluid flowing through the pipe?
Nigel