http://www.seat61.com/
http://www.ferroviedellostato.it/
http://www.sncf.com/

TGV trains are great, every American should ride one to see how high speed rail ought to be done.

When I was in France (2001) you could take a boxed or bagged (they call the bag a "housse") bicycle on TGV trains, the box/bag had to meet certain size restrictions. My box was over the limit, but I was allowed to take it on anyway. Lots of local trains accept unboxed, unbagged bicycles, but you have to check the schedule to make sure the train you're taking will accept bicycles. Italian high speed/long distance trains do not accept bicycles, but lots of local/regional trains do. Once again, check the schedule and make sure the train you want accepts bicycles.

Sticking to the coast might save you some climbing, but you'll miss a lot of very pretty country and probably find yourself riding through more urban areas than you want to.

How long do you plan to take? Are you camping, staying in hostels and hotels, or a mix of the two? Are you going to spend some time sightseeing, or just treat this as a purely athletic endeavor?

The Lonely Planet Cycling Guides to France and Italy would be excellent resources, even if you don't follow the exact routes laid out in these books.