It is a little difficult to see exactly what you have in your model as the tree is mostly closed. But here are some things to think about.
– Use Named Selections. It looks like you have some defined already. You will want surfaces defined for inlets, outlets, important planes and also volume definitions for regions that will have different properties such as porosity, density, etc.
– It looks like you have some contacts between your bodies. This will help you identify the interface between the different “bodies”. Did you use the imprint option (in the geometry tool) to ensure the contact faces have the same bounds?
– If you want a 1:1 nodes across the bodies, as opposed to an non-conforming interface, then you will define these as a multibody part (again back in your geometry tool).
– I assume you are using the Patch Independent because this is coming from a scan or something that has lots of tiny faces, edges, etc. If there are edges that you do want to keep defined, you can put a Named Selection on them and the mesher will resolve these.

And a completely different thought, have your tried meshing this directly in Fluent meshing? It does pretty well with “dirty” geometry. Plus there are controls for proximity, so you have better control of how many elements are thru thin parts. If you are new to ANSYS Meshing, it may make more sense to move into Fluent Meshing and just start learning that tool.

A very interesting problem you have there!