Option 1
All by train until Slovenia. So, Option One has you taking a train from Krakow to Prague, then from Prague to Bratislava, then to Budapest and then back to Vienna and then to Slovenia.
Since your plan is a train from Vienna to I am guessing Ljubljana I am curious why you don’t just take the train from Budapest to Ljubljana so you don’t have to backtrack to Vienna?
But I suspect you have a reason to do with timing. So, moving on, Bratislava isn’t much of a visit in a day trip. Generally, I think time spent in Vienna or Budapest is better spent, but at least you are willing to give it some additional time, that’s good because It does become a better place when you get beyond the tourist shtick of the old town.
The logical order, if nothing else is going on that influences it, is Krakow, Prague, Bratislava, Vienna (or Vienna then Bratislava – doesn’t matter), Budapest, Ljubljana. All by train.
Option Two
The way you propose it requires renting a car. I wouldn’t do Cesky Krumlov with a rental. Take the train.
Then again, the question of why first to Budapest and back to Vienna? With the shuttle service you can go on to Vienna (Budapest too actually). The logical order, if nothing else is going on that influences it, is Krakow, Prague, Cesky Krumlov, Vienna, Budapest, Ljubljana.
Also look at Regiojet trains for this trip. Less expensive and nicer trains.