I don't remember all details of our Mad drive: 24 Hours of Le Stans, but I think that the border guards will squeeze you in someone else's car, compulsory, for all crossings between CIS-countries. To Afghanistan and Iran there are indeed long border walks.

If your travel agency can NOT provide a cross-border car, I would consider doing the whole trip individually. It is easy to find a local driver in every city / at every border for ca. USD 100 - 150 per day.

Some other points to consider (maybe not for the OPs specific itinerary, but for other Stan-travelers):

At Bishkek Airport most nationalities get a Kirgiz visa-on-arrival.
In Bishkek you can also get the Tajik visa (incl. GBAO permit for the highly recommended Pamir Highway) within 24 hours.
Kazakhstan is now visa-on-arrival for many nationalities AFAIK.

I am saying this especially for the luxury hotel travelers here, because if one is already in the rather frugal Stans, one may want to profit from the few excellent hotels, like in Almaty (RC or IC), Dushanbe (Hyatt Regency or Serena), Bishkek (soso Hyatt Regency).

Not only hotels are a pain in Uzbekistan and Turkmenistan, but also visa applications. And the Uzbek border guards are the world's 2nd most obnoxious. They will, for example, fleece you on exit, and you are in trouble if you carry more cash than on your arrival's currency declaration. We had to go back and "spend" the surplus (buried 1.000 USD under a tree; retrieved upon return from Afghanistan ).

Nevertheless, great countries to travel to.