Could the word order here be 'Kdo těch šedesát knih koupil?' ?
why are we using the genitive case here
koupím něco / něčeho ?
shouldn't it be: kdo koupil ty šedesát knih?
Numbers above 4 are followed by genitive. The demonstrative is considered to expand the word "knih" hence it agrees in the case.
What's the difference between kupoval and koupil?
Koupil is perfective, that means he bought it once at a certain point in time. Kupoval is imperfective, mostly implying repeated action.