Swizerland, Italy and Austria

I think you should fly into Zurich and out of Vienna. Is that your plan?

Innsbruck is between Zurich and Salzburg, so stop there first.

I think you could eliminate Zurich and go directly from Chur to Innsbruck. You could spend the extra nights in Luzern, Lake Como, or Vienna. Zurich is OK, but there are other destinations on your list that are more interesting and deserve more time.

That's 8 different hotels in 15 nights. Do you really want to do that much moving around? I know Milan isn't overwhelmingly loved on this forum (whereas I found lots of interesting museums there), but Vienna--surely Vienna is worth more than 2 nights/1 day?

Don’t base in Interlaken. Get UP into the mountains in Wengen or Murren. You won’t regret it. If budget is an issue, look at cabins at Camping Jungfrau.

Are you planning to fly from Zurich to Salzburg? I’m a bit confused by the return to Zurich after the Bernina Express. I think I would go from Wengen to Chur (or Pontresina), take the BE to Tirano, then continue to Varenna.

Skip Milan and go to Innsbruck, Salzburg, then Vienna. Fly home from Vienna. Add any extra nights to Vienna.

That much moving around is going to leave you very little time to actually see anything. Every time you move you lose atleast half of a day, especially when you're moving such great distances, so your 1 night stops are going to leave you with basically a late afternoon/dinner before packing up the next morning to move again. If you're set on seeing all 3 countries in 2 weeks, I'd recommend flying into Vienna and out of Milan or vice versa and condense some of your stops. Personally I'd only do 4 places in 2 weeks, but if you really want to cover all that ground, perhaps something like:
Vienna - 2 nights
Salzburg - 2 nights
Innsbruck - 2 nights
Luzern - 3 nights
Wengen - 3 nights
Lake Como - 2 nights (fly out from Milan, no need to stay there)