Hi there!
I have been living in Tajikistan for 1.5 years and know particularly well the North of the country where you are going.
I would like to warn you that your Day 1 is very ambitious. It will take you 30 mins to get to Hissar and about 1 hour to visit the sights there. It will then take you about 3 hours to get to Iskandarkul. If you want to enjoy the place, you will need to walk around or go up to some of the Zerafshan Valley villages higher up which will take you 1 to 2 hours. Please note that from Iskandarkul to Penjikent it is another 3 to 4 hours depending on your driver and the road conditions at the time. So if all goes well you can expect to arrive in Penjikent at 10 PM (given that you will need a lunch break and some time to get out from the airport). Please note that from 8 PM it is dark and I would not recommend driving in the dark on the road to Penjikent. Instead of sleeping on Penjikent, I would recommend that you either sleep in one of the homestays in the villages above Iskandarkul or in Ayni. Howestays are cheap (about USD 10 per night and about 5 USD for diner) and give you the real experience of a night in Zerafshan. Ask your driver I am sure he can help you organize one once you are in Iskandarkul. Ayni, which is on the way to Penjikent and about 45 mins drive from Iskandarkul has a single hotel in the outskirts of the town and the night in the single room should cost you about 100 somonis.
I would then devote your Day two to Penjikent and would probably spend the night there. Again there are some German Agro Action homestays there that will not cost you much.
Day 3, you should make a early start (like 7 AM) and you can hope to be in Istaravshan at noon, eat there and visit the town, especially the market and its handicrafts. Within an hour after Istaravshan you will reach Khujand. Do take the afternoon before you take your flight to visit the city. You will need to leave for the airport at around 5:30-5:45 PM so try to get to Khujand around 2:30, to have 3 hours to visit its market and mosque (in front of each other) and its nice museum in the old fortress. If you still have time have a fresh juice or a beer at Vyssol restaurant in front of the museum. It is a very nice place. As for the night in Dushanbe, I am not sure about budget hotels. Our consultants usually stay in relatively pricey guest houses. Do stroll around Dushanbe at night after you have arrived and have had dinner. It is safe and most of the sites will also look good at night! Just do Rudaki from the Chaikhana Rohat down all the way to Opera Ballet, for the most interesting sights. Have a beer there and some shashliks in the cool Moscow Park.
Day 4 - check the museum opening time. You may not be able to visit it if you want to be at the airport 2 hours in advance. Note that it will take you about 10-15 mins (depending on traffic) to get to the airport from the Museum.
Have a nice flight and possibly bump into you on the Khujand-Dushanbe flight as I will be on it too! Cheers!
