I visited Krakow (4 days, including 1 for Auschwitz) then Prague (3 days) and then Cesky Krumlov (2 nights, 1.5 days) in early October. I think other respondents have led you well to visit 2 cities, and I agree that your new itinerary looks wise.
Can you please specifically mention what train it is from Praque to Krakow
I used seat61.com for guidance on all the connections for my 18 day journey. He gives you all the options, advantages and recommendations, and even pictures of trains and stations. His accuracy was remarkable! (And easily verified when you go to the respective booking sites.)
I chose the overnight train from Krakow to Prague (opposite direction that you are traveling.) I booked a single sleeper compartment, with WC (and shower, which I didn't use) for security as a solo female traveler. I loved everything about the experience. It saved a day of my itinerary for sightseeing, and I slept very well - ready on arrival in Prague for a day of sightseeing. I am a light sleeper; the rocking of the trains did not bother me and this tourist route has only 1 other stop, at Oswiecim (Auschwitz) - (very) early in the morning in the direction you'll be traveling. If you don't think you'd sleep well, there is still the daytime option as your current itinerary shows.
Will the above schedule allow a trip to Cesky Krumlov, or don't bother
I was very glad to have 3 full days in Prague before going to Cesky Krumlov for 1.5 days. This felt relaxed and allowed me to see what I wanted in both places. CK is lovely, and a day trip is doable. It really depends on the length of your must-see list in Prague. If you decide to go to CK, choose carefully whether to go on the Monday in your itinerary. As RS points out, most sights in CK are closed on Monday, though the town (the main attraction) and the castle grounds are always open. I enjoyed being in CK on Monday as it was MUCH less crowded from tour groups than the Sunday afternoon I spent. But if you are interested in tours of the interior of the Castle and Baroque Theater, those are closed on Mondays.
Seat61.com also has details for the inexpensive train day-trip from Prague to Cesky Krumlov. I pre-purchased and printed that ticket at home, there is no need to book in advance. Knowing your options and the train times, you could wait until you're in Prague to decide whether to go to Cesky Krumlov.