1. Place for stay- everything depens on amount of money you want to pay for it. Hotels which are located close to Rynek Glowny are quite expensive and you have to book them many weeks earlier. But on the other hand... you are in the centre of this beautiful city. Close not only to museums, but clubs and restaurants, too
This link should help you to take right decision:
2. I know only one GOOD model store in Cracow- it's PHANTOM located close to Rynek Glowny (Slawkowska 13 street). They have very helpful staff and they can speak English.
3. Unfortunately I know only two military related museums in Cracow:
Armed Forces http://www.krakow.pl//kultura/instytucje/?INS_TYP=2&INS_ID=180
If you want to learn more about Polish Army- you should visit Warsaw.
4. Excellent place for your wife will be Royal Casttle http://www.krakow.pl/en/turystyka/?id=wawel.html
Hope it helps.