Take the earliest train out of Manarola so you can gain some time in Florence (skip Pisa it's very touristy). I think you will love Florence based on your interests and it is very easy to get around. I would take a day trip (either car rental or tour) to Tuscany. San Gimignano is a favorite and you can use your hiking skills (it's like San Francisco, all routes are up hill). Also, there is a nice hike up from the Boboli gardens to overlook Florence, a great hike at dusk.
One full day in Venice is enough in my opinion. Plus you have nearly a whole day on travel days. The train from Florence to Venice is only 3 hours so you can take an early one and be settled in your hotel in time for lunch, a siesta and then go out in the evening. I do agree staying on the islands is ideal if you can afford it. I stayed at the Hotel Certosa and really enjoyed being close but apart. Hotels are cheaper in October so splurge a little in Venice and skrimp a little in Florence. October is flooding season in Venice. Make sure you bring one pair of good shoes just in case. The 12" high platforms that you will see all around town are not benches...they are walking paths in case it floods. Don't panic, flooding is normal and the Venetians are experts at handling it. Don't pack an umbrella...just wait for the African immigrants to magically appear with ponchos, umbrellas, and little plastic bootie things as soon as the rain starts. I was in Venice in October two years ago and it didn't rain at all but my mom was there the year before (to get married) and it poured and flooded a little.
Some other tips:
Venice pass not worth the cost...but get a vaparetto pass and use it like a tour bus. Rick even has an audio recorded tour of the grand canal based on the vaparetto boat/bus. There are a few must see things in Venice but really just plan to wander the side streets, get lost. Also for the the really good food in both Florence and Venice you have to wander away from the tourist paths. The restaurants south of the Grand Canal are a great place to have dessert and watch the sunset. but the dinner isn't great
The Florence pass, totally worth it. Lines can be long even in October and the pass really helps.
Use the TrenItalia website (not RailEurope) to research your train times. You don't have to book in advance, in fact, I recommend you don't so you don't have to rush to meet a specific train. You'll have to use the Italian station names. Florence = Santa Maria Novella, Venice = Venezia Santa Lucia (not Maestra which is on the mainland). Freccia and Italio trains are the fast ones.