@Anonymous, most of your model looks very good and clean. But I think I found the issue. It resides here:

The issue is you have two faces which are in direct contact but are not "merged" to form a seam. This would be fine if they were two separate parts, because Inventor would just create a bonded contact between the two and would know that it needs to match the mesh between the two faces. But because this is a un-bonded seam between two faces on the same part, Inventor doesn't know quite what to do. It pointed to certain holes as the problem area, but those holes are fine.
Here's what I did and was able to get a mesh using the default settings without any problems: I just used "Delete face" with "heal" enabled and deleted the small face that touches the larger face pointed to above. I've attached your part with this modification made. Basically, doing this bonds the two faces together and creates a seam. Your sheet metal functionality won't work right with this done, so you'll need to suppress the "Delete face" feature once you're done with your FEA.
Making this change only affected one constraint (Flush:2). I personally would flush two of the Origin Planes (the XY planes in this case) rather than faces on the part. This is more robust and will hold no matter what features you change or remove on your parts.
Hope this helps, let me know if it resolves your issue.