Hi! Now you have a good layers structure (I just don't see the reason for the top layer duplication, but you see better) As Doug says, each line is not a single layer, Illustrator is not like Photoshop here. Each line is like a book on a shelf, where the shelf is a layer. You can select some objects in a layer and group them, so you will decrease the first-level step of the structural complexity. If you need to get any specific object, you'll see it in the group. If you want to collect all the objects at the top layer, just select them all and group them, they all will move to the top layer. If you want to finally have the one united object, without separating to small details, follow Doug's advice: select all, call the Outline Stroke command and then use Unite option on the Pathfinder panel. But I would suggest doing this at the last step and primarily saving an editable copy for any further tasks with this image.
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