Just spent 2 weeks in the Alps in Austria, Slovenia, Italy, and Switzerland. First trip and I have to say the cycling of a lifetime.
Comments about trains already given above are pretty accurate and sound like based on experience. The Lonely Planet cycling guides are very good reading while preparing for the tour. Camping in France and Italy is incredible...clean, cheap, and warm showers. Usually have a WIFI connection for just a few Euros. Every town seems to have an associated campground with a store and restaurant with reasonable prices. Nice thing about most if not all alpine passes is the hotel/bar at the top where you can get a cold beer and lunch. Climbed the Stelvio and the Forst beer tasted incredibly good after the 48 switchbacks.
The roads are smaller in Europe and drivers tend to drive very close to you so you can't be a nervous nellie and for heavens sake get any thought of "take the lane" out of your head...it is all a delicate balance. The drivers really like you it is just that there is less room (damn we are spoiled here in the US). And the motorcycles are about as bad as a swarm of black flies...Just ignore them.
And Last but not least get some heavy duty touring tires with real rubber treads. The crushed rock on the side of the road can and will cut into the best road tires. I used Continental Contact 700x32c (but they make 28c as well) and had zero problems...one of the riders had a something Brown tire and it worked. The one rider with Conti 4 Seasons got a major cut from the rocky shoulders.
Oops not so last...Get an i-phone and an account with AT&T. You can call from anywhere in Europe but, you can get on WIFI and Skype (even if the person doesn't have a camera phone) for just a few cents a minute to anyone back here in the US. In addition you can have music, download books (lonely planet?), and the phone has an incredible camera...I don't have one yet but my 2 friends did and was able to use the phone to call my wife for pennies. I am just waiting for my contract to get closer to ending and will be switching over (I have been with my current carrier for 6 years) but without the iPhone what the heck. With what I know now I wouldn't hesitate switching even if it cost me to buy out the contract.
This was my first European tour and I wouldn't hesitate going over with an open itinerary and just a general idea of where I wanted to ride. Try and schedule the ride for late May early June or Sept/Oct. The summer in the lowlands is incredibly hot. Good luck and I hope this has been a help.