Great travelplans man. I am kind of curious if you got your visa for Turkmenistan in meanwhile. Me, I am now in Varzaneh, a town close to Isfahan and consider the same travel as yours by hitchhiking. The choice is now between Turkmenistan-Uzbekistan to Tajikstan - Or via Afghanistan to Tajikstan > Kirgistan.>
For Afghanistan, double check if you can get a visa on the road. Some Embassy's ask for a personal interview in your home of residency - the only embassy you can apply.
So I'll suggest you across Turkmenistan. I have been denied my transit visa without a reason. I applied together with some Belgian guys and they got it. I'm on my way back to Azerbaijan to cross to Kazakhstan by ferry.
Courage and all the best!