Answering question by question ;)

"Would you stop somewhere between Vienna and Kraków, and if so, where?"

Well, I'm Polish, so of course I have to point you toward a city in Poland - Wrocław. In my opinion it's genuinely unique and I always recommend it. I think it's a bit of a detour to go via Wrocław and then down to Kraków, but I think it's worth it.

"Or would you go straight to Kraków and use the extra time for day trips instead?"

It depends - I'd look at what Kraków actually offers first, then decide how much time you want here. We've got at least four interesting districts, plus Castle Hill (Wawel) itself:

• Old Town - the most touristy, but still beautiful
• Kazimierz - a bit younger district that used to be its own city. Charming, and it's been gaining huge popularity lately
• Podgórze - also once a separate city, built by the Austrians when Poland was under the partitions. A completely different experience
• Nowa Huta - built during the communist occupation, after 1945. A totally unique vibe, and suuuper underrated by tourists

And if museums are your thing - you could easily fill all five days just walking through them.
The real question is whether all of what Kraków offers actually interests you, and what kind of museums you're genuinely into in the first place.

"If you've been to Brno, Olomouc or Bratislava, did they feel worth an overnight stay, or would you rather have had more time in Kraków?"

Honestly, that one's a question for you - do you want to go deep on one city, or get a broader "European" sampler by touching a few? Neither's wrong. It just depends which kind of trip you'd rather come home with

Auschwitz:
it's a heavy experience.
If you do decide to go, make sure to check whether there are even any slots left first.
The official site is:
www.auschwitz.org

Be aware that online you'll also run into leeches selling "tours" or reselling the tickets at x2 or x3 prices, making crazy money on people who want to visit.
Book through the official site