Connecting Cinque Terra with Nice and then Spain/Portugal

1) If you have no urgent need to go to southern France, then the best way to get from Italy to Barcelona is to fly. Discount airlines fly out of Bologna, Pisa, and Florece to BCN. Check whichbudget.com for the one that suits you best, and the sooner you book, the better deal you get. Rail travel from Italy across southern France to Spain is, to say the least, slow.
2) August will be crazy busy in any beach area on the Iberian peninsula. For that reason (among others) I would go back to Madrid for a few days and do a day trip to Toledo. There is no direct connection by train or bus from Sevilla, so you'd have to go back thru Madrid anyway. And Madrid is one of the great cities of Europe.
3) No...in fact, things will be jammed. If you have not booked your Alhambra tickets in Granada, do so ASAP at www.alhambra-tickets.es . The Alhambra is the most popular tourist site in Spain, and with much of the country taking its summer holidays in August, it will be very busy.
4)Transportation in both Spain and Italy is relatively inexpensive and convenient. Trains in Italy and Spain and, additionally, intercity coach in Spain. For rail tickets in Spain, you can book significant discounts at www.renfe.es up to 62 1/2 days in advance...most bus schedules, fares, and tickets are available at www.movelia.es.

Off topic...to me, Genova is too far north for CT and Pisa. Why not base yourself in La Spezia or one of the other CT towns for that time?
Also off topic...if you have no pressing need to go to Valencia, leave it off your list...far better to devote more time to the other Spanish stops on your itinerary. You can fly cheaply via Vueling or Spanair from Barcelona to Granada, then pick up your itinerary there.

That's great. Lots of good info. New questions though:

1/ I checked my Eurail schedule from last summer (dated I know, but I figured travel times would be pretty much the same), and the train rides between CT-Nice and Nice-Montpelier and then Montp-Barc didn't seem that bad. 4 or 5hr rides, which I'm ok with. Has this changed??

2/ I'm kind of being stubborn on the Madrid and Portugal thing. I really want to get a taste of both countries. I guess my next question is if I want to see Granada, or skip it and add it to my time in Portugal. Keep in mind I'm not into museums all that much (Rijksmuseum in Amsterdam was amazing though) Thoughts? Granda with more spain vs No Granada + Lisbon and Algarve. I will have 3 days in Madrid regardless of which option I choose.

Thanks for the flight links. A 30euro flight ticket for 3hr flight is definately worth the hassle if I need to get somewhere fast.

And I'll check out other spots in CT. La Spezzia is worth checking out!!

Thanks again

If you miss Granada, you are missing probably the greatest Spanish heritage site there is. I would give up Portugal if it meant missing Granada.
you say you will have 18 days from CT, and you plan to spend three nights of that in Nice. If you also stop in Montpellier, that makes 4.
I think you will find that the train from the CT, or Genoa, to Nice, is going to run closer to 7 hours than five. That'll mean another day gone. From Nice to Montpellier is between 5.5 and 7 hours....another day gone. And from Montpellier to Barcelona is 4.5 to 5 hours....about half a day gone. So to the four days you plan to spend in Nice and Montpellier, add, say, two more days for travel, bringing the total to six. Add 3 days in Barcelona, and you are now down to 9 days.
Granada for 2 days and Sevilla for 2 days leaves you five days...simply not enough to do justice to all the other places you want to see. You will spend almost that entire five days on the move...and it's not easy to get from Sevilla to the Algarve. I still think your best bet is to head back to Madrid for the last five days, and do day trips to places like Segovia, Toledo, and Avila.
I assume you are considering a Eurail pass. Remember that many of these trains will require mandatory reservations, which is an extra cost, and many national railways limit the number of reservations available to passholders, so there is a chance that reservations for your trains might not be available.

Thanks man, great info. It looks like travel around this part of Europe is a little different than what I've experienced in other parts I've been to.

So I think I'm leaning you're way with cutting out Portugal. Here's a new question that assumes you have been to Venice: I can only choose Venice if it means leaving out one of Seville or Granada???

A simple answer....no. But that's just MHO.