Alpine Passages
Having spent almost 10 years studying minority cultures in Northern Italy, Austria and Slovenija, I have to ask you what you motivation for this trip is. It is easy to get lost in any one of the several remote regions of the alps for years at a time due to the fact that many of these areas are unknown to the outside world.
Consider this alternative: Forget the Milan to Berlin concept - these destinations are too far apart in so may ways (culturally, geographically, etc.) and ask yourself which experience you want to immerse yourself in. The Milan-Berlin concept covers a ton of mileage, but it takes you through the intersections of several cultural areas, as opposed to the epicenters of those cultures. There are three language groups alone (Cimbro, Mocheno and Ladin) that meet in the main valley of the Alto Adige River that runs the short distance from Bolzano through Trento down into Lago di Garda near Verona.
Should you select one (or three) of these cultural areas for immersion, you could string together a series of loops, each one fully exploring the terrain and people of a unique cultural area. You could coordinate train segments between them, to get you to the "Cultural Zones" faster, and miss the long stretches of Italian Autostrada (the absolute worst scenario for cyclists) and enjoy narrow, winding roads that connect hundreds of villages along the way.
If this is something you would consider, I'd love to share my cycling experiences with you in these specific regions. Not everyone is a fan of "thematic adventures", but having cycled through almost all of these regions, I can assure you that they are not to be missed. You would be like the second foreigner to ever come rolling through many of these villages.
Enjoy the planning - it's one of the most exciting parts of the experience!