We have made the trip to Paleohora many times, both from Plakias and also direct from Heraklion airport. From Heraklion airport to Paleohora takes us exactly 3 hours (broken down it is an hour from the airport to Rethymno, and hour from Rethymno to the Paleohora turn off at Tavronitis and a further hour from there down into Paleohora. From Plakias the drive is about two and a half hours, but I agree that the ferry is more enjoyable, particularly if you can break the journey at Loutro. The last ferry into Paleohora arrives there at 6pm, in comfortable time to find a room (plenty and reasonably priced), grab a shower and enjoy your evening volta before your evening meal.
Jan