Your journey sounds amazing!
I would definitely recommend Krakow and Warsaw. Warsaw is a wonderful city, and I would probably say my favourite in Poland due to the buzz and big city feel that you get there. I'd give yourself a few days to go and explore as it is a big city with lots to do and see. There are Bierhalles in Wroclaw, Krakow and Warsaw, and do be aware that it is a Polish chain. The beer is very nice, but it's on the expensive side for Poland, and I definitely wouldn't recommend the food there as it's decidedly average.
When I went by TLK train between the two cities, the train was fairly quiet (Me and my two friends had a cabin to ourselves, an there were a few empty ones). We went on a Saturday, outside of the holidays. Buying a ticket in Krakow was easy, but we used the ticket machines which have instructions in English to avoid going to the ticket desks. I would recommend using the machine, you can also use them to book in advance, and to reserve seats.
The other city in Poland I would highly recommend would be Wroclaw. It's about 5 hours 45 minutes from Krakow on a VERY slow train. Ours had a buffet car, which came in handy for a drink. We went back to Krakow on a coach which in comparison was cheaper, had wi-fi and took only just over 3 hours. Wroclaw to me didn't seem like somewhere where you can spend more than 2-3 days as you will have seen everything by then.
I've never been to the Polish coast, so can't recommend anything there.
I think this is the best site to look up train schedules.
http://rozklad-pkp.pl/bin/query.exe/en?
It lays everything out clearly, is in English and makes it clear if you have to change train or similar. It also gives the price, but you can't book here. You have to book here
http://rozklad-pkp.pl/bin/query.exe/en? But when we tried it didn't work. Don't know if it's working now sorry.