Try Mercy Corps, http://www.mercycorps.org.
I’ve no up to date names or numbers as it was 1999 when I did a comission for them but they were really good to work with.
You could also try http://www.hopeandaiddirect.org.uk/ who I’m sure will put you in touch with a local contact.
Also lightstalkers member Andrew Testa is based in Kosovo and was helpful when I was doing my disertation at university.
Hope this helps.