I have the opportunity to visit Dounoussa and Koufonisia in early September. Based on the ferry days and times it looks like I can either plan on:
5 Days in Donoussa
2 Days in Koufonisia, or

3 days in Donoussa
4 days in Koufonisia

Any advice? 4 days seems a bit too much for Koufonisia, and island you could walk around in a couple hours, while 5 days I may find myself repeating myself in Donoussa. Anyone who's traveled to these islands, advice would be appreciated. I know this is largely down to personal preference but I would welcome others' experiences in this regard. I am solo traveler.

IMO 4 days is too much for Koufonissi (it would be fine for each of the neighbour Islands Heraklia, Schinoussa and Amorgos, however).
May be you didn't realize that there exist also connections with a stopover at Amorgos:
every day: KOU dp 12.40 - Amorgos (Katapola) ar 13.10
almost every day: Katapola or Egiali - Domoussa. Egiali can be reached from Katapola by Island bus.