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I need the portion of the image in the rectangle to be its own layer, where I can edit it or move it. I am a newb with Inkscape and would appreciate some guidance.

I've read that Path> break apart should be my solution, but I'm not getting anywhere after I select the edit path nodes tool and select the inner & outer lines of the area I am trying to separate from the rest of the image. I am not sure if I am shift-key selecting the right nodes because after I choose Path> Combine, nothing happens. There's a TON of nodes!

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Create your trace, as you've done. With the fill turned off, also as you've done, the results should be as you require. Perform the following:

Select the rectangle, use Path, Stroke to Path, which will convert the rectangle to path.

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With the rectangle selected, shift click on the traced path, then use Path, Intersection to create the portion you require.

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Trace it manually. That means redraw it, but have the original as locked in the bottom for reference

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It's useless to fight with Inkscape's automatic tracing if you expect easily editable result. Inkscape traces even thinnest lines as filled areas, never as simple strokes. In addition the number of generated nodes is often frightening high as you have seen. You have no control how the shape is divided to parts except by tracing the shape several times in differently partially erased or recolored versions. This preparation must be done in a photo editor.

If you redraw it Use different colors for different parts. It's up to you to decide which parts should be separate. If you can assume the shape is LR-symmetric, you can well draw only half of it and combine the halves

Be informed that practicing a little with the Pen and the Node tool will pay the used time back generously, probably with 10000% interest.

Use preset shapes such as circles, rounded polygons etc where possible. You can combine them with path operations and edit them with the node tool. There's no need to use the pen for everything. In addition preset shapes often are already symmetric.

Preset shapes must generally be converted to paths for easy node editing because in Inkscape they are not Bezier curves. Use Path > Object to Path.

A practical path editing hint: more likely remove nodes than insert them more. The less you have nodes the easier it is to get nice curves.

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