How do I fix factory reset problems

About a month ago I acquired my first virus. I went into safe mode and factory reset my Mac. I had a Time Machine backup from about a week before the virus and was able to reinstall my most critical files. I no longer seem to have the virus. However I still have problems that seem to be due to the factory reset. In the order in which I became aware of them:

1. I had lost disk space and so didn't have space to restore my photo, audio and video files;
2. The system installed was Monterey though I had previously upgraded to Catalina. It doesn't seem to let me upgrade past Monterey now; and
3. I have recently tried to perform a Time Machine backup and it refused claiming I have duplicate Macintosh HD disks (Note NOT Macintosh HD - Data disks). In opening Disk Utility, I find a Macintosh HD volume that contains two Macintosh HDs (one of which contains another Macintosh HD with only 15.6 GigBytes of data), none of which I can unmount as hovering over their hyphens gives "This operation can't be performed, because you can't unmount the startup volume." I also have a Macintosh HD - Data volume that contains another Macintosh HD - Data volume, with hyphens that are not grayed out and let me start unmounting them but soon fail, but stops early in the delete.

This prompts the following questions in the order of decreasing priority:

1. Is there any way I can do a Time Machine backup?

2. Is there any way I can further upgrade the OS?

3. Is there anyway I can get more disk space?

4. Are these symptoms associated with other problems I should be aware of?