I don't think you can really shoehorn Cesky Krumlov into that itinerary and do it justice. The whole point of going there is to explore the surrounding area also and use it as a base for day hikes. However, for only a day or so when you have just 3-4 days in total you're taking a significant detour to a place which is not as well served with transport connections as the other places on your list.

I would replace it with somewhere like Pilsen, which is super easy to get to from PRG, but you should definitely allocate more time to Brno than Pilsen if you do this (1 day for Pilsen is fine).

For travel I would definitely use a bus service like RegioJet (Student Agency) - very convenient and cost-effective. Good service and you can cancel up to 30 mins before free of charge (I used this last week and got the refund to my credit card promptly).