Follow Chani's advice, it's good stuff. I used to say to not run yourself ragged, that 3 cities in 8 days was borderline crazy. But then I put myself in the mindset of first-timers with the excitement of finally seeing what they've been reading about all these years, and with the Freccia trains (2 hrs Venice/Florence, 90 minutes Florence/Rome leaving pretty much every hour), I thought, whythehell not?!
It almost sounds like you've already booked the air, which per upthread states that you would be in Rome during the Mother Teresa canonization. That could possibly hike hotels more than the usual already-exorbitant rates. If you haven't done the air and can reverse the trip, starting in Venice and ending in Rome, so much the better. If not, then scour for a good hostel. As you said, I do think on the average that you may have a difficult time finding a decent hotel for under $100/night. $150, maybe. And yes, B&B's may be more to your liking cost-wise.
Back to the trains. Start looking on the Trenitalia site now for discounted fares. Can't remember without checking, they let you book ahead either 90 or 120 days in advance. However, remember that the caveat for the discounts is that there are no changes that can be made. You book it, you ride on that train at that time. We did it no problem, printed out all the pertinent info online, had our hard copies with us.
I've used TripAdvisor for hotel and B&B reviews, and they haven't steered me wrong yet. I do book through the actual hotel site rather than a third party, however.
Finally, all-inclusives are fine but there's no thrill in planning, which is half the fun here. Embrace it!