Transiting Between Countries

The best guide to train travel in Europe is www.seat61.com where you will find a lot of answers. Vienna-Bratislava and Bratislava-Budapest are easy by direct train. To and from Cesky Krumlov will be a bit more complicated, but perfectly doable.

Vienna — Bratislava is about a 1 hour train ride. Bratislava to Budapest is about 3 1/2 hours on the train.

Use the Trainline App. Put in your departure and arrival destinations, scroll down to your date, hit the “Find trains and prices” button, and you’ll be shown the available trains - with cheapest and fastest identified - and can buy tickets thru the app.

There are a number of shuttle services out of Cesky Krumlov that transport people daily from Prague to their quaint city. And they can get you to Linz where you can catch a train to Vienna. They're easily found online, and they're priced reasonably.
We took a 39 mile bus ride into the main Vienna train station from Bratislava.
The train ride from Bratislava to Budapest is a pretty ride.
Be sure that no Bratislava taxi driver takes advantage of you getting to the train station. Ours drove us all over the place when it probably wasn't more than 3/4 mile to our hotel.
I wouldn't worry about booking train tickets ahead of time.

Rome2rio is a useful tool for exploring transportation options between places. It has links to carriers. The carriers' own websites will have more reliable info about specific schedules, prices etc., and it's safer to book directly with the carriers. But Rome2rio can get you started in the right direction (so to speak).

We did the same route a few years ago. This is how we (4 adults) went
Prague - cesky K by car with ckshuttle.cz
cesky to Vienna same company
Vienna - Bratislava by hydrofoil. We walked to the boat from our hotel. We used the Slovakian company, LOD.sk, 1/4 the price of the Austrian. Same waterway (on their website swipe left for the Vienna to Bratislava route, it’s 25€ one way, 90 minutes)
Bratislava - Budapest by bus, it was called Student Agency now called RegioJet but website is studentagencybus.com
From Budapest we went to Zagreb by bus.
No trip was very long, easier then getting to an airport with all the layers of security.

We used CK Shuttle a few years back for connections from Prague to Cesky Krumlov and then to Hallstatt. The drivers are prompt, professional, and speak great English. The company uses small vans and it is door to door. It's costs a little more than public transportation, but sometimes it's nice not to have to work out all the transitions.
Have a great trip!

Thank you to all, really helpful tips.

seat61 has so many details, maybe I'm not using it right but finding the info I need wasn't amazingly easy.

Haven't downloaded trainline yet, but will be great to have an app like this. I've been struggling one without going through individual companies.

Already using rome2rio for rough transit time for different transport methods but already finding these to be really unreliable. Good to see which companies do particular routes though.

LOD.sk doesn't mean to do that route anymore, but I did book through Twin City Liner. The rest we'll look at trains as buses aren't our preferred method.

Regards,
Kurt

Just go to the website of the national train company of the originating city and book your tickets a few days prior. It will ve easy and not confusing.

And for Cesky Krumlov connections also look at CK Shuttle and Bean Shuttle: I think easier and more convient (relatively short van rides)