I travelled from Tajikistan and the Fan Mountains to Almaty in between 2-3 weeks in August and September.
If you fly into Almaty, I would hitch or get a shared taxi out to Castle Canyon (long walk, 10km, but should be a fair few people and it's well worth it - there is also a covered area at the bottom by the river where you can sleep - sleeping bag needed - and make sure you have enough food and water)
From there you can hitch to the border, only another hour, pick up some food in the town before the border, and you can sleep on the steppes either side of the border if needed (villages either side if you haven't got a sleeping bag and mat, or if you're lucky a local herder might invite you to their yurt, I declined so I could enjoy the stars - which were stunning).
From the border to Karakol could be a challenging hitch, but there were a fair few vehicles, plus I managed to get a ride in a shared minibus to the village about 2km from the border, so there is some public transport.
Save a few days for Karakol and try to get some trekking or riding in, I didn't and regretted it, the lake isn't really worth it, plenty of better ones for getting your feet wet in.
Karaol to Bishkek is easy - Sakura Guesthouse is nice, cheap and fairly easy to walk into town from. Watch out for dodgy police in Osh Bazaar (pretend you have no idea what they're saying, your passports are at your hotel because you have just arrived, and then be polite say goodbye and walk off, they're unlikely to follow you) but don't let it stop you visiting, one of the most characterful ones I visited.
Bishkek to Osh is a fairly long drive, it can be broken at Toktogul, but beware it's about a 5km walk to the lake, which is lovely and warm, and we managed to hitch most of the way there and back, but getting onward transport can be a challenge (I was with a group of four others at that point, so it wasn't hard).
Osh is pleasant, enjoy the last sense of civilisation before the Pamirs.
From Osh get a shared taxi to Murgab - amazing drive - make sure your driver does most of the talking etc at the border and it should be straight forward.
Murgab is pretty quiet, I stayed in the newish hotel in the centre of town overlooking the bazaar which was cheap and easy bargaining!
From Murgab it's worth trying to hitch with a truck, can be hard going, but well worth it, usually space for two in each cab, and it gives an unrivalled view point. Just beyond Jelandy (couple of km) is a major truck stop (they just park alongside the road) but will visit a small white building on the right hand side (from Murgab), which has a great hot spring - you'll need it after all the bumping around on the road - and they offer very cheap beds, no food though that we found.
If you're lucky enough that your driver stops you should be able to hitch with them to Khorog, if not there should be other trucks.
In Khorog stay at the Pamir Lodge and you're sure to meet other travellers who you can share with on the way to Dushanbe, or more ideally down to the Wakhan (I didn't have time to go,m but I've heard it's well recommended)
The drive to Dushanbe is long, but stunning, try to do as much of it in daylight as you can - nice views of Afghanistan in the early stages.
Dushanbe is expensive, cheapest homestays are $20 min, and there is no hostel, worth a stop for a night, maybe two, but then head up to the Fan mountains. I went to Iskander Kul - and it was beautiful, and very cheap to stay at the Turbaza there - but not much to do for more than a day. I'm not sure what the trekking options are from here, or being able to drive through to the Fan Mountains proper - worth a look.
I believe you could then head up to Anyi and back into Kyrgyzstan (not sure of the border situation) and to Bishkek or Almaty to fly home, or go back to Dushanbe and fly from there, or fly from there to Almaty or Bishkek as those flights would be the same as going by land, but alot quicker.
When I was there (a month ago) the Penjikent border was shut, but if that re-opens you could swing by Samerkand (well worth it) and fly from Taskhent.
If you don't fancy the above, you could easily go through Uzbekistan, get a transit visa through Turkmenistan (enter at Turkmenabat, exit at Nukus) and loop back through Uzbekistan and Kazakhstan. Turkmenistan was my favourite 'Stan by far
Have a great trip!
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trip report: awesome month in Tajikistan, Aug 2015
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