Actually, this is your third question. In yWriter, there are several ways to exclude scenes from export. For example, you can set for each individual scene whether it should be exported as text, RTF, LaTeX or HTML. Another possibility would be to control the export via scene tags. All this applies if you use the built-in exporter of yWriter and convert the exported file to ren'py using a custom postprocessor.
If you convert the yw7 XML file directly, you also have the option to store Ren'py specific metadata in senes of a special type, e.g. "Notes" or "ToDo". This is then easier to keep track of within yWriter. Furthermore, a separate XML parser gives you free access to all metadata stored in yWriter.
If you don't need to change the document structure when converting to ren'py, but need more metadata or structural information than provided by the regular yWriter export, you can also try my
template-based HTML exporter and remove the HTML tags from the scenes with a postprocessor.