Hi Leah, I am going to give you advice that I haven’t done myself - LOL! I love Italy and have been there numerous times but only travel by train. Since you will have a car and are traveling off-season, would it fit your personalities to book your lodging as you go? The reason I am suggesting this is that the northern lakes can be very rainy, like a downpour! I speak from experience. ; ). And I think Cinque Terre at that time of year probably won’t have the hiking you want open. If the weather is better in one portion of Italy as you’re there, it would give you more flexibility.
Although I like Siena more than Lucca, if you stayed in Lucca, you could swing over to Cinque Terre for the day and at least see it.
I would pick Perugia over Spoleto that time of year. I stayed at Locanda della Posta Boutique Hotel there and recommend it. This is my trip report that year which has some good activities for Perugia, https://community.ricksteves.com/travel-forum/trip-reports/trip-report-please-do-not-comment-until-i-change-the-title-filling-in-the-report-thanks
I really liked staying in Ravenna, plus it gives you the chance to go into the Basilica di San Vitale as soon as it opens to enjoy before it’s crowded. Last time I was there, the experience of standing there enjoying the stunning mosaics in silence was amazing! ….at least for the first 15 minutes.
Have a great time!