Badgers, I suggest you start with a clean sheet of paper - your itinerary as listed above is unrealistic and will lead to misery.
Before getting into details, it would be helpful to provide some basic info...
When exactly are you going? (hope it's not real soon...you have lots of work to do)
Have you ever been to Europe before? (I'm guessing no, based on your first stab at an itinerary)
Next - be honest: how many FULL days do you have in Europe, not counting the day you arrive nor the day you depart (which you should not count as usable days, no mater what time the flights are)?
That number of full, non-travel days is how long your trip really is - and then you need to figure out how long to linger in each place. Remember, every time you move form one place to another, you lose from 1/2 a day to a full day. Be sure you allocate some time to each place - you're not going to "see" (or experience) anyplace unless you spend at least one full day there, and that's a bare minimum. Minimize "one night stands" - remember, you'll get a lot more out of any place that you spend 2 or more nights.
You're flying in to Krakow and out of Florence...OK. So those are your end points. Get out a map - one you can draw/write on. Draw a line from Krakow to Florence - your actual route may twist and diverge from that somewhat, but probably not wildly so.
Next, I suggest you make a list of places you want to see on this trip. Locate those places on the map. Draw a dot on the map for each place you want to visit, but only make a dot for those places that are more-or-less along that line between Krakow and Florence...you can add some dots that are a bit off the line, but not any that are far from the line.
Then, look at how you might logically "connect the dots" - by train, bus, rental car*, flights. With no doubling back, no wild loops waaaay off the route. Yes, you can include flights to jump from one city to another (so your actual route doesn't have to be contiguous), but anytime you do a flight, subtract a day from your available time (getting to the airport, flying, getting settled) will consume pretty much a full day. Moving by train will consume half a day, if you're efficient and on your A game.
You will need to make trade-offs and painful choices - that's what everyone has to do. The faster you move, the less you see and experience...it may seem paradoxical at first, but it's true. Slow down and you see/experience more.
The above should get you started on the process towards a more reasonable plan. Then you can tweak and refine it. Hope that helps - and good luck!