Hi,
My suggestion would be to limit how much traveling you do. To me it seems like a lot of traveling. I understand flying into where its cheaper. I would recommend staying a night or two in Lucerne, Switzerland as you will enjoy the scenery and can travel up the mountains. In addition I would do Lake Como and spend two days there exploring the towns near the lake. Bellagio and Varenna were truly lovely.
We LOVED Florence and it is near Cinque Terre which is also great. Venice to me seems a bit out of the way for your trip but thats just me......
Rome is awesome we had spent four nights there and felt we got all we could out of it.
You mentioned Salzburg.......Have you considered flying into Vienna? Flights were reasonable and Vienna is awesome and you can easily train it to Salzburg and maybe even stop off in Innsbruck.
Munich we loved, although there are also other places in Germany that we preferred (Baden Baden, Heidelberg, Rothenberg (sp))
All in all map it out and try not to waste time traveling between too many places. If you can save Venice for a day or other trip where you would pair it with Croatia or go to Dolomites up north then do it then.....