I took several independent trips to Europe with my mom, beginning when we were just a few years older than you two, so I wish I could be more helpful. I can't really give useful answers to many of your specific questions.
I spent 2 months in Italy last summer, and I walked about as much as Pam did. It's very nice to be able to combine some outdoor walking with city sightseeing, but I didn't do much rural walking on my last trip except up in the Dolomites. It was terribly hot in June and July except up in the mountains; I hope you'll be luckier with your September trip.
There's no indication that your mother has limited mobility (and she's younger than I am), so I think you'll have no difficulty. Just be mindful of sunset when walking in the country. My mom was very slow (undiagnosed emphysema), and we almost ended up on one of the Cinque Terre hiking trails after dark. That would have been dangerous.
I'd be hesitant about going to Sicily for just a few days. I loved it and spent about 18 days there (could have used more), but it's a bit of a slog to get to unless you're already down in the toe of the boot. If you do decide to go to Sicily, I'd try to include a few days in and around Siracusa as well as the Etna walk. Some others would prefer Taormina, but it was just too overwhelmingly touristy for me to want to spend more than a few hours there in June.
The Amalfi Peninsula is stunning and there are surely some nice coastal walks there.
If you're looking for a southern area that's a bit off the beaten path (not claiming it's undiscovered), take a look at Lecce in Puglia. It's a lovely Baroque city, and last year there were reasonably-priced van trips, booked through the city tourist office, to surrounding towns, including Alberobello, Matera and a number of little white coastal towns that reminded me a bit of Greece. I assume there are still van trips running in September, but they are based on demand and flexibility is required. If not, side trips by public bus are possible to many of the same locations (probably not Matera); you just can't hit as many in one day. Lecce is at least 5:10 by train from Naples, however.