About territories that the KR still reigned after the Vietnamese invasion: Were there any atrocities committed? Did the Khmer Rouge still follow their agricultural plans, or was it completely different to the Democratic Kampuchean Regime, if so, how?
No, they've stopped. The agricultural plans were changed and they became more reasonable. I'd love to write something more, but I haven't brought my books to my apartment yet, so I can't write anything specific.
The conflict after 1979 was a completely diffrent period in terms of political alliances and possibilities to enforce ideas of Khmer Rouge. After that year we've got multi layered conflict between KR supported by the West, China and Thailand on one side and Phnom Penh backed by Vietnam and USSR. It was a typical proxy war (or for most time proxy conflict, without any major fights). It's hard to enforce social ideas during war, especially if they were proven so ineffective during the DK regime.
Morover, I don't recall any books on the situation in Khmer Rouge controlled areas (those on the state controlled by pro-Vietnamese communists are also very rare). There is little or none data.
Unfortunately this question violates the 20 year rule, as only a tiny fraction of the time period you're asking about was 20 years ago, and then just barely.