The ferry from Baku to Kazahkstan may be a problem as the schedule is erratic and it may only leave every week or two. You will not find out a departure date until you arrive in Baku and visit the ferry terminal. The ferry from Baku to Turkmenbashi runs several times a day and aside from the difficulty in getting a ticket, it was an enjoyable journey.
Also, Azerbaijan may only give you a 3 day transit time for your bike, you can either quickly transit though the country and leave within 3 days or overstay this period like we did (by a week) and receive a lot of grief but a very small fine. Make sure you have these issues squared away before you board the ferry or you may miss it.
You can't go from Armenia to Azerbaijan either. These countries are still technically at war and the borders are closed between them. No border crossings between Turkey and Armenia as well. The only way to get into Armenia is via Georgia or maybe Iran. You will have to do Turkey-Georgia-Armenia-Georgia-Azerbaijan. Be prepared for some grief when the Azeri border officials find out you have visited Armenia.
I did the Caucasus and the 'Stans last summer, its an amazingly memorable place to visit and I can recommend it. The GS should be fine, although in Kazahkstan it could be a big problem from Aktau (where the ferry drops you) as I have heard this track is a nightmare.
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