Hiking CT and Pisa in 2 days

You could start your hike in Monterosso, and stop in Vernazza for lunch, and then head on to Corniglia, and catch the train to Manarola (perhaps my favorite, altho we stayed in Monterosso). Sleep in Manarola. The only trail open between Manarola and Riomaggiore is the upper trail (not along the coast). It goes up up up, and then down down down. This would give you time to hang out in Manarola in the morning, and have lunch in Rio and walk around and then catch the train.

I did not take any ferries, just hiked, so cant speak to that. We did almost what I describe. There is a rock that people cliff jump from in the port at Manarola (check youtube) that you could do when you arrive the first night. IMO, for the short time you have, Id skip the ferry; stay active, be out in the scenery, but different strokes :)

Thanks for the suggestion Jessica. That is what I actually planned on doing! I haven't booked lodging in Manorola yet, but I expect it to be pricey because it's one of the more popular CT towns?
I didn't think the ferry would take up too much time if I chose to go on one?

The only trail open between Manarola and Riomaggiore is the upper
trail (not along the coast).

That goes for the lower trails between Corniglia and Manarola as well: only upper trail(s) will be open.
The 2 segments of the SVA2 (blue Path) between Corniglia and Riomaggiore are closed.

As you are needing to book a room very late in the game for the CT (accommodations fill early for high season!) I'd take whatever is still open in any of the 5 villages which suits your budget. As you don't want to be hauling your luggage on the trails, you can always catch a train back to your village of choice.

If you haven't found the park website yet, it'll be helpful for trail map and route descriptions:
http://www.parconazionale5terre.it/Eindex.php

CURRENT trail info (this can change at any time depending on weather/damage:
http://www.parconazionale5terre.it/Esentieri-outdoor.php

Cinque Terre passes for hiking any segment of the SVA2:
http://www.parconazionale5terre.it/Ecinque-terre-card.php

Thanks Kathy for the links. I will check them out.
I may go back to La Spezia for the night since their hotels are about 50% cheaper.

You might also consider staying in Levanto, which is one town north of Monterosso. I just got back from staying there (again) last month. Should be cheaper there two than the five villages; it's not a picturesque town (from the water) like the five villages, but it's a nice town. (The ferry serves Levanto also, a few times during the day.). If you want, you can hike (no hiking pass required) between Levanto and Monterosso - about a 3 hour hike. At one point you can see all five villages below - amazing view. Should be less crowded than the hikes between Corniglia and Vernazza or between Vernazza and Monterosso.

The best hike is the steep one between Manarola and Corniglia via Volastra. The views are AMAZING, but it's quite a steep climb up from Manarola - a zillion steps up. (If it matters, no hiking pass required for this one either.) I just did this hike last month for the first time. The trail was not empty - there were plenty of other hikers but I wouldn't call it crowded.

Thanks for the suggestion Andrew. I really don't care for where I'm staying for the "night" to be picturesque. I'm just going there to sleep, nothing more. In my original itinerary, I had actually book a train from Florence to Monterosso that arrives around midnight. I booked lodging in Monterosso, but then I realized that I could just stop in La Spezia, and stay there for the night, and train to Moneterosso in the morning. No sense in paying 2-3x more for lodging in Monterroso.

Is the trail (the one via Volastra) still open?

What do you think about the ferries? Are they worth it for scenery?

Looks like you plan to take the 8:51pm Freccia to Rome (last train of the night to Rome). You might want to pre-purchase that ticket now as Super Economy tickets are available for 14.90 euro, or about one-third of the Base fare. That fare won't last long.

Is the trail (the one via Volastra) still open?

As of three weeks ago it was open. Trails in the CT can close on short notice due to slides, etc. however.

As long as you can handle the steep climb up, up, up a thousand steps, it's really a great hike, amazing scenery down.

What do you think about the ferries? Are they worth it for scenery?

The scenery is of the towns, approaching them from the water. If you have time, I'd take a ferry, but not if you have to wait around for an hour because you just missed the last one or something. If you are a hiker, I'd focus on the hikes. The towns will be crowded during the day, though they are worth exploring a little.

@Frank. Yup, I already booked it for 14.90 Euros. I paid 3x more for my Venice->Florence ticket.
For future reference, when can I expect cheaper super economy ticket sales?

@Andrew. Ah I see. I should be able to handle it. I think my only concern may be the heat and humidity, but I should be fine.
When you say "ferry," are we talking about the ferries designated for transporting between CT towns, or specific ferries for sight seeing?

Yes, by "ferry" I meant the one that goes between the CT towns. I don't think there are too many other ferries that run very often - didn't see them, maybe there are a few that run a few times a week or something. Maybe more in high season. But with the limited time you have, I wouldn't bother with those at all.

I suspect the price of that specific train is low because of the departure time. Most people would want to travel earlier in the day. It's actually the best Super Economy fare I've seen in quite some time, so I think you just got lucky. I used to get 19.90 euro Super Economy fares from FCO to Florence and 9.90 euro Super Economy fares between Florence and Bologna, but I haven't seen fares that low for a couple of years. The best Super Economy fares are usually offered when prices are initially posted about 4 months in advance. Recently Italo has been offering better discounted fares than Trenitalia, but Italo runs less frequent trains on fewer routes.

Yeah I've seen Italoreno is generally cheaper, but they don't have many, or any, late night or early morning trains between my destinations.

My Venice->Florence is a early morning train, and I think I paid about 42 Euros for just a regular seat. Is Venice->Florence generally more expensive than Rome->Florence?

The economy fares sell out quicker on the more popular trains - so even Venice-Florence will have some trains with cheaper fares last minute at unpopular times.

FYI, if you aren't in a rush, some of these routes have options that use regional trains instead of the faster trains. They usually take longer and may require more connections...but they are the same price at the last minute as they are ahead of time. (And can't sell out - no reserved seats.) Not speaking specifically about Venice-Florence, but you can always look for the regional options when traveling last minute and see if they work for you. Sometimes, they have for me.

Trenitalia fares are based on distance and Venice-Florence is longer than Florence-Rome. Your 42 euro fare is obviously a discounted fare, and you may be able to get a lower discounted Florence-Rome fare especially if you travel early or late. Whether it will actually be cheaper depends on which discounted tickets have sold out the day you want to travel.