A few random things I remember from the trip:
First, Slovakia was awesome. We did the itinerary basically as I posted it without the night in Bardejov at the end. We also did not make it to Kosice. Each place we visited was great and I would recommend them all. Starting in Banska Stiavnica, we primarily stayed in and ate at penzions. They almost always had things for kids to do, ranging from a basket of toys to playgrounds and trampolines.
Janosik Days in Terchova were a particular highlight. It was like a small carnival or fair with tons of great folk performances. We could hardly get our four year old away from the performances until we promised her she could ride a couple of the death traps.
We visited both Orava and Spis Castles and they were both excellent. The tour at Orava was tough because it was in Slovak and quite long. I'm not sure whether they have English tours available but we basically showed up for the last tour of the day and there wasn't much flexibility. Spis had English language listening devices so we got to go at our own pace.
My German served us well in many places, but enough people spoke English that we would have survived.
My wife particularly enjoyed trying many different versions of halusky. She makes a dish at home we call halusky with just noodles and cabbage. Since she is vegetarian, I doubt she'll change her recipe, but she happily ordered it and picked out the bacon all over the country.
Most of our hotels came from Lonely Planet. Some were particularly welcoming or well situated and I'll list them.
Banska Stiavnica - Penzion Prijemny Oddych
Terchova (really in Stefanova) - Chata Vratna
Levoca - Oaza - a tremendous bargain and quite nice
We had booked hydrofoil tickets from Vienna but when we got to the launch we found out the Danube was partially closed to pull at a sunken boat. We ended up taking the bus, which worked out fine. It dropped us off very near where the hydrofoil would have. We walked to the Sheraton. It was a long walk given that we had a 4 year old, an 11 month old, a lot of luggage and a carseat, but ordinarily it would be fine.