Harribobs,
Plakias to Rethymnon is about 40 minutes
Rethymnon to Chania is about an hour (at least every hour)
Chania to Paleochora, as you say, is about 2.5 hours I think, but it's a scenic drive through the mountains.
So about 4.5 hours plus waits in between. You would have to plan to meet a specific bus from Chania to Palochora.
The boat from Paleochora leaves about 8.00 or 8.30 and gets to Chora Sfakion about mid-day. The bus back to Plakias would be about 5.00 pm.
In June I am planning to do most of this more leisurely, i.e. fly to Heraklion, bus to Chania - stay overnight - bus to Paleochora - stay a few nights - boat to Sougia - stay a couple of nights - boat to Chora Sfakion - maybe stay overnight, maybe not - bus to Plakias - stay a few nights - various buses to Matala - stay a few nights - bus back to Heraklion.
Greecemad.