Special border permits in the Stans
 

I want to motorbike around the Stans (Kyr, Kaz, Taj and Uzb), but I'm confused about permits for special border zones.

From what I can figure out, if I:
1) Stay away from all Chinese borders
2) Use main border crossings between the Stans
3) Don't go off the beaten track near any borders between the Stans

I don't need any special permits?

That's pretty much it. You can always approach a border crossing on a main highway, you only need to be eligible to cross into the next country (i.e. have a visa, if you need one). Aside from the crossings it's good practice to stay out of border zones, though what precisely constitutes a border zone is not always well defined or marked. Sometimes it's unavoidable, e.g. parts of the M41 in Kyrgyzstan which track the Uzbekistani border, but you are fine on a main highway.

So in short, follow your own guidelines and you'll be fine, no border permits required.

EO

You may want to get the additional permit for the GBAO region in Tajikistan when you apply for the country visa, it's worth getting to be able to visit the region.

If you want to do Pamir hwy you pretty much need one for Tajikistan; it's only $20 more when you apply for eVisa online no need to do anything special.

There is at least a dozen of checkpoints along M41 IIRC