Caravanistan

I am early on in my thought process for a trip combining Tajikistan and Turkmenistan. I would like to do this overland and use public transportation. I am curious as to what border crossings involving Uzbekistan and if there is a general best way to approach. Areas of interest in Tajikistan are khujand, istaravshan, dushanbe area. Areas of interest in turkmenistan include Mary, Merv area, gas crater, and Ashgabat. Ideally I wouldn't be using a tour service other than perhaps stand alone transportation a to b or a day tour.

Depending on time I may try to visit Baku at the start or the end of the trip.

Thanks for the input. I am a us citizen with us passport.