Itinerary Recommendations

You are young, so I won't give my usual spiel about staying longer in fewer places--the 20s is when to do a fast paced trip like this. But, I would make some tweaks. I would press on to CT on arrival day and not bother with the back and forth to the lakes. I would eliminate Padova and Verona and spend two full days in Venice. I would arrive in Milan on day 11 unless you have a particular interest in something there--you could then add a day to somewhere else. One more day in Tuscany would be nice. Be careful about what you leave in the car when exploring, and make sure you understand about ZTL. Good luck!

As many people advise, consider how many nights you have, not days. Your itinerary has too many destinations for such a short trip. Consider spending two nights in Varenna, so that after you recover from the flight, you can explore the area. Venice deserves two nights.
Padova and Verona both on the same day and then taking a train to still another destination is a lot. I would really try to narrow it down to a few places that interest you the most. Slow down and enjoy each place. You are young and if you find that you like Italy, you will go back.

You're going to spend a lot of time on the trains, including getting to and from the stations. Not much time to actually enjoy the places you go.

7 different locations for overnight stays in 11 nights is far too fast paced

You are not considering how much time it takes to change locations-check out, get to train, travel time, find lodgings, check in, get oriented
At least Half the day is gone
Lather rinse repeat

Day 10 sounds especially miserable

Slow down

To give you an idea . . . .

Get on the train in Varenna and arrive in Riomaggiore

1. Take 7.35 am train, 3 train changes, arrive 6 hours later
2. Take 8.35 am train, 2 changes, 6.5 hours
3. Take 10.35 am train, 2 changes, 5 hours

You get off the train at approx 1.30, 3.00 or 3.30 pm.

Drop a car in Florence and train to Venice. I only looked at Hertz locations. All the city locations close at 6.00 or 6.30 pm. Best would be the airport, closes at 10.30 and you don't have to drive in city traffic. Then tram to the train station and 2.25 hour train to Venice. 1 hour minimum from last stop in Tuscany to airport, 1/2 hour to return car and get to tram by shuttle bus, 20 minutes to train station. You still have a 2.25 hour train ride and then get to hotel.

Those may be the 2 longest journeys. Work out how much time you will be in transit (remember you have to start and end at the hotels with your luggage) each time you move and how much time you have for hiking and sightseeing.

That's the reason most of us think you have too much travel and not enough time.

I'm exhausted just from reading this itinerary. This is more like a travel marathon rather than a vacation.

I suspect you meant Riomaggiore. These towns are small and "exploring" them is a pleasant uphill/downhill stroll for perhaps an hour.

Otherwise, there is great advice on modifying your trip in the other comments.

If this were my trip:

Day 1 - arrive Milan, train directly to Venice. Have a nice dinner and sleep.
Day 2 - Venice
Day 3 - Venice
Day 4 - Venice in the morning, train to Florence
Day 5 - Florence
Day 6 - Florence
Day 7 - Early morning train to Riomaggiore, with stops in Pisa & Lecco.
Day 8 - CT
Day 9 - CT, late afternoon train to Milan
Day 10 - Milan
Day 11 - Milan

My two cents: I agree with all who said there are too many stops for this amount of time, especially the first night. Unless all you want to do is literally see the lake, I would remove this from your itinerary. If Lake Como is a must, you should spend at least two nights. Day 4 is doable, although others have advised against Pisa and Lucca in the same day. We did exactly what you're planning as a day trip from Florence and it was fine. I also agree that Venice needs more time. I have no experience with agritourism, but I was considering it for our trip and two things come to mind: many do not allow one night stays, and I think to really enjoy the experience, one would want to do more than just sleep there.
One food recommendation: do Alessandro's cicchetti "pub crawl" in Venice. Food was good, wine was ok for what it was, but you're there for Alessandro and his hysterical distain for Americans!