This is a great itinerary with ample time to see the local wonders without rushing.
For staying in Kampot or Kep, I would choose Kep without hesitation. And you can visit Kampot and the pepper plantations easily from there. To reach REP from there, flying is definitely the best option in your case and flying from KOS and PNH are both viable options. If you stay in Kampot, KOS is closer. If you are in Kep, PNH is a good option and has the advantage to have much more flights. A transfer Kep to PNH should cost you around 80 USD.