I visited Uzbekistan, Tajikistan and Kyrgyzstan but it was always separated trips.
Penjikent to Isfara in less than one day but I'm not sure you will have a lot of departure in the afternoon...
I mean from Isfara to Batken because you will use a shared taxi.
If you are agree to use one as contracted or at least to pay for the "missing places", it will be much more easy.
Then for the all trip, I think three days or at least two and half...
Michel