I just crossed from Batken (Kyrgyzstan) to Isfara (Tajikistan). No problems at all, just a brief passport/visa check, nobody was interested in the luggage. Exceptionally easy for Central Asian standards!
Some remarks:
- Drivers at the bus station in Batken pretend that there are no marshrutkas going to Isfara, just chartered taxis. This is not true, but the marshrutkas do not depart from the bus station. They leave from somewhere in the town centre, in front of a government building - just ask.
- Batken is a very boring place, feels like the end of the world. Isfara is much livelier. So if chosing where to stay overnight (if needed), take Isfara.
- Uzbek exclaves are no more a problem, Kyrgyzstan has built good new roads around them. In Tajikistan, however, the road on to Khujand passes briefly again through Kyrgyzstan. This can't be avoided, but there are no checks.
Here's my detailed report:
https://passportparty.ch/2017/07/13/border-17/