What you did should work and is what I do all the time. There appear to be two problems.
Firstly, point 12 is a problem. If you didn't send any new books to the device when it was connected, the "Processing" shouldn't have happened. This generally means that one of the books you put onto the device in step 5 wasn't processed correctly in step 7. When that happens, the device stops processing more books and none of them appear in the library list on the device. When you reconnect the device and open calibre the books are shown as on the device. The next time you disconnect the device, it tries to process the books again and when it reaches the bad one, it stops again.
The only fix for this is to remove the bad book and try again with the others. Unfortunately, finding it can be a pain. I believe the books are processed in alphabetical order by the full file path of the file. Finding and removing the first book that isn't shown when using the device, should solve it. Hopefully, there isn't another one.
The above might be causing the problem with the series information, but it shouldn't be. To see what is happening, I need more information in the form of a debug log. To do this:
- Open calibre
- Go to the device configuration screen. At the bottom is a field "Title to test when debugging". In the field, put the name of a book already on the device that has series information in calibre.
- Save the changes.
- Restart calibre in debug mode. Do this by right-clicking the preferences button and selecting "Restart in debug mode".
- Calibre will restart and display a message about debug mode and a log.
- Connect your Kobo Touch.
- When calibre finishes the sync ("Jobs" in the bottom right shows zero and the icon stops) close calibre.
- The debug log will get displayed in the editor. Post the contents of that or PM them to me.
The log will give me an idea of what is happening and hopefully how to fix it.