This is what I mean:
Looks like you have overlapping geometry. Try this: in Edit mode, select all with A and press M. Choose By Distance.
If that doesn’t work, try adding a remesh modifier and turning down the voxel size
The modifier crashed my computer…
And it didn’t seem to work.
How small did you choose the voxel size to crash you computer ?? And i think there are some bad normals involed…can you show your first image in wireframe mode and also showing amount of vertices (Blender Preferences → Interface → Staus Bar → Scene Statistiscs)?
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did you try the clean tool? it is found in the mesh near mode selection.
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Hi there 
I think you lost that many faces with merge because you had one big big face connected to many random vertices, so it was like a random concave island in there.
Your geometry is not so complex. If I were you, I would turn on face orientation to check if the outside is nice blue everywhere, then simply select the vertices and hit F to create nice flat faces for the holes. (You can subdivide edges as well if you search for subdivide, should you need vertices someplace).
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