My Itinerary of Europe trip in April (Details in description)

I don't have much knowledge about this area, but I think this is a great post because it includes all the necessary information and you did your research homework first. I've always read that Cesky Krumlov should not be done as a day trip.

Good planning. April is not a good time to visit Switzerland.

We have traveled the region many times. I agree with above that April is often a hit and miss time of the year in mountainous regions as rains often come with the changing seasons. On the other hand, we've had some glorious weather early April in Innsbruck.
We prefer to travel Austria for our mountain fix because it's easier and cheaper to travel thru--than Switzerland. Getting there thru Munich is also very easy.
Your planned itinerary is pretty aggressive--going to so many places. But could you consider taking them in this order:
Budapest
Vienna
Prague
Cesky Krumlov
Hallstadt
Salzburg
Innsbruck
Then you could take a 2 hr. train back to Munich and fly out of there.
You might do best if you used one of the fine Cesky Krumlov shuttle services to get you to C/K and on to Hallstadt. If you're looking to reallocate a night or two, you could cut C/K to one night and cut out Hallstadt altogether. The other cities in the area (like Munich) are just more important cities to see.
There are many ways to look for rooms. With Air BnB, it's often hit and miss. We usually book B&B's through Booking.com for simplicity's sake. PM me as I know a couple of really good, inexpensive places to stay in Budapest and Vienna.

I think your itinerary is doable and I'll go even farther and say it will be enjoyable. My only concern is that I'm not sure how Innsbruck would be in April. If you choose to dump it or reduce time spent there, I'd add to Salzburg, Prague and/or Budapest.

For accommodations:
Vienna--I LOVE Hotel Austria, though for some odd reason they do not seem to be answering emails as of late
Prague--Hotel Hastal is quite reasonable with a substantial breakfast. It's centrally locally and the folks are great.
Budapest--Best Western Parlament Premier, spotless, great breakfast, reasonably priced, not quite as central but was fine for us.
Salzburg--Hohenstauffen. Close to train station and a pleasant 15 minute walk to old town. Great price, huge and delicious breakfast, great folks and family run.

David, your plan is great.

Thanks David and Jules for the recommendation. I will adjust my itinerary accordingly. Thanks to everyone for responding. And David let me figure out the itinerary and appreciate your help in figuring out the accommodation.
Cheers
Prague

I don't think this trip is rushed at all. In fact, it's quite generous the time you're giving to various places.

Depending on your interests, I might take one night from Innsbruck and add it to Salzburg or Vienna. I love Innsbruck but there's not a ton to occupy you more than two full days at most unless you're looking at some day trip outside. Salzburg is also small, but there are daytrip opportunities galore. If you drive, I'd recommend renting a car in Salzburg to fully explore the area including dipping up into Germany. If not, I'd still consider a trip to the Eagle's Nest and Berchesgaden via Bob's Tours.

As someone who's visited most of these places multiple times and all of them at least once, this seems like a great trip!

Thanks Sarah, I have kept Innsbruck as a base for the Austrian Alps. Is there a better base for the alps in your opinion. I am not into skiing and would be highly interested in photographing scenic landscapes. Many thanks.

If you want to hike, do photography, and see the Alps then your 3 nights in Innsbruck makes more sense. I've never been to a city where you can go from the center to the top of a mountain entirely via public transit so quickly. It was a marvel. The sights in the city can be seen in a long day but the non-winter hiking options seemed limitless.

Salzburg is also well-located but the accessibility without a car to the mountains is far better in Innsbruck.