Catania is, indeed, gritty around the bus station. It improves greatly over near the cathedral and university. Definitely worth some wandering, and the markets are interesting.
I enjoyed all of Noto, Ragusa, and Modica. Noto was pleasantly quiet when I arrived before 10 AM. It is quite small, but the walk from the bus stop to the historic area takes 5 or 10 minutes.
It's a bit of a scramble to figure out the bus schedules. Verify that you won't encounter any holidays, and check on the meaning of any symbols appearing on the schedule. Sometimes the tourist office has printed schedules to give you, but always try to confirm the return time and pick-up spot when you arrive.
It is wonderful to wander around in Ortygia. I made multiple side trips from Siracusa and didn't allow enough time for Ortygia itself. It needs a lot more time than Noto, even aside from other sights in Siracusa.
For me the top sight not included in your itinerary is the Villa Romana del Casale outside Piazza Armerina. It's a Roman villa with stupendous mosaics. Your schedule won't permit a trip there by public transportation, but I thought I'd mention it in case you happen to run into someone who offers you a ride.
A few thoughts on food:
The classic granita in Noto (Caffe Sicilia or Dolceria Constanza are commonly recommended) is mostly almond with a dollop of very strong coffee granita on top. Only occasionally available elsewhere in Sicily. I don't remember the special name of that combo, but I'm thinking about my late breakfast of granita and brioche right now.
The food in Sicily is very good in general, with stronger flavors than you tend to get on the mainland. The pastries are good, too. I had been in Italy for 3 weeks by the time I reached Sicily, so I was looking for food that was interesting as well as good, but not too expensive. I found two places memorable enough to recommend:
If you're hungry in Modica, I can vouch for Basilico. I see that Trip Advisor reviewers liked it, too. The menu is more interesting than the restaurant's simple though stylish appearance would suggest. The address is Corso Mazzini 2. It's visible from Via Marchesa Tedeschi, which seems to be the main drag. By the way, have a map of Modica (electronic or paper) with you. The bus didn't drop me off where I expected, and I had considerable difficulty orienting myself.
In Ortygia/Siracusa I lucked into a real find, which is also well known to the Trip Advisor crowd. Locanda Mastrarua is at Via Vittorio Vento 11, not far from Via della Maestranza. That's roughly midway down the peninsula on the east side. This is more of a white-tablecloth spot. The menu doesn't seem to be online, but I think there were 5 meat, 5 seafood, and 5 vegetarian options for each course. Maybe it was only 3 of each. In any case, I opted to eat there twice. It's small and is obviously known, despite the off-the-beaten path location. It can fill up.