I think your bigger problem is flying with LOT. While they seem decent enough to get you there in one piece, their on-time record, in mine and many others experience, is less than stellar. You can almost depend on them running late. So a tight connection with them is always a bad idea. Give yourself some time because they also don't seem like the type to be anxious to bend over backwards to get you on another flight. Their customer service is also a little lacking. But the price is fantastic, I'll say that.

That is too long in the Krakow airport, but also bear in mind that Krakow city center is not particularly near the airport. We were just there last month, it seemed like it was what, maybe half and hour, depending on traffic? So there's at least an hour there, but still it would be worth it I think. Have a great time, Warsaw and Krakow are both fantastic.