1. Krakow to visit Schlinders Factory and also to visit Auschwitz, but how do we get to them?
The Rough Guide to Poland explains how to get there. There are also excursions advertised in Krakow, but it's better to buy the rough guide before you go for two reasons. Firstly, it's much cheaper and more interesting to get there yourself, and not difficult if you follow the instructions and secondly Polish guided tours tend to be wordy to the point of dreariness and slanted towards a Polish point of view on history. Better to go on the train and join one of the free official tours. One warning though - it isnt a tourist attraction; it is an emotionally crushing place and you should think carefully about whether or not you really want to see it.
Krakow isn't dangerous. A safe city, even in the scruffier suburbs and very safe in the touristy bits.
what is Warsaw like? We plan to visit Wolf's Lair when we are there, has anyone here been before?
I'm a bit biased towards Warsaw since it's my home. Nevertheless it's certainly the most cosmopolitan and cultured city in Poland with far more to see and do than any of the others and there's a good contrast between the pretty bits in the Old Town and Royal Route and the communist era buildings in the strict centre of town. You might like Warsaw and since your post suggests you like wartime history there's much more of that to see in Warsaw than anywhere else in PL. The newish Uprising Museum is interesting and the Jewish Museum should be open soon. However, if you want to visit the Wolf's Lair (actually not that much to see) you should stay in Gdansk - it's a long way from Warsaw. Gdansk is also a good place to visit.