As said above their are really countless options depending on your interests.

You can get to most places with public transport, however you will struggle getting over the pass on the east side of wakhan. If you want to go to wakhan using public transport the best option is to go to khorog and then take public transport from there to langar and work back through the valley to khorog. Once in the valley there is some transport and hitchhiking is quite easy.

So something like:
OSH - karakul - MURGHAB - bulunkul - KHOROG (capitals are the places you will need to stop, lower case are additional options). Then from khorog you can go to wakhan. You can go all the way east to langar on public transport and work back. Lots of options here, but many of the places just need an hour or 2. Yamchun fortress is one thing not to miss in wakhan my opinion (you could day trip there with public transport from khorog).

Then between khorog and Dushanbe you can side trip into bartang valley. You can read about it in this thread https://www.lonelyplanet.com/thorntree/forums/asia-central-asia/tajikistan/independent-travel-in-bartang-valley

Tajikistan and the High Pamirs (edited by Odyssey) can be useful even if it's not a "new" edition.

This book is fantastic and I can't recommend it enough. It is perhaps not a travel guide, but more a complete history of the area and culture with a few travel tips.

There is also some nice trekking opportunities around osh (alai region) or you could go to sary Mongol and visit peak Lenin.

You really need to research the options and come up with a route. Once you have a route we can give you better advice on how to do it and transport options.

Follow the advice above.
You ned to be lucky to join a group on the way and it can be time consuming to find few people in Khorog to have your "own" group.
It will be better to use a mix of public transports, shared jeeps, hitchhiking and contracted lifts.
Moving around is much more time consuming than challenging or difficult.
But time can't be the issue.

Michel

Hi Altona,
We were in Central Asia this year from mid May to mid June. We hired a car from Dushanbe to Osh (9 days). Since we had room in our car, we did pick up a female solo hitchhiker from Murgarb to Osh. It all depends on luck and who you meet on the road.

Regarding special place, the entire Wakkhan and Pamir stretch was the highlight of our Central Asia trip. People in Tajikistan are very hospitable. If we have to name a few favorites, they would be:
- Hike and homestay at the Jizew village
- Bulunkul lake in late afternoon and take a bath in the warm spring nearby (after a sand storm that day!)
- Hike to the Engels Meadow (we didn't make it all the way to the meadows as we had a late start and had to return back to town, but the scenery was magnificent)

suggestion - bicycle the Denali Park road - if you are interested in wildlife
if starting your northern route in Fairbanks - I suggest staying at Sven's Hostel/campground in Fairbanks - good location and people - very experienced motorcyclists and bicyclists meet here - excellent advice to gather
there is an excellent laundry, shower, campground on the road heading north maybe 20 miles from Fairbanks
the mountains are very steep along this road but I assume that you are in excellent cycling condition - you and your bike
do not underestimate the remoteness of facilities along this route - there is a place to get gasoline just on the north side of the Yukon Bridge (which also has the pipeline fastened to it )
no trucker will pick up a hitchhiker - and there are few RVs that I have noticed in my travels north - towing bills for a breakdown in the far north would cost thousands of dollars and you can not simply abandon a vehicle - A flatbed hauler would have to take a vehicle back to Fairbanks at great cost
Coldfoot is the only place to get gas or food and there is a visitors center on the other side of the highway - it is super interesting - Wiseman is a bit further north by a river - population maybe 10 people or less. I never saw much traffic on the haul road at all
some tour groups travel as far as the marker for the Arctic Circle but that parking lot is a bit of a let down - many tour buses turn back from there - it is a very long ride to Deadhorse at the end of the road
Atigun Pass is very steep and considered to be an avalanche zone - no stopping - but there is no easier way between heading north or south - the further north you go the flatter the terrain - hence the name North Slope
I saw quite a few musk ox and the northern lights were splendid
as someone mentioned you will need permission and a guide to past the guard gate on up to the Beaufort Sea or part of the Arctic Ocean or whatever.
maybe that bit will cost around 75 dollars - I do not remember - if you choose to stay in lodging at Deadhorse it will be very pricey - but you can probably find camping somewhere before you get to Deadhorse
You will not be allowed to take your bike past the guard house - sorry to be negative but I think you will have a great trip !
if any interest here are a few pictures I took in the area
http://www.dutchpickle.com/alaska/alyeska-pipeline-and-musk-ox.html

I crossed from Kazakhstan into Kyrgyzstan in June. Here is some updated information:
- Shared taxis for Kegen depart from Almaty's Seyakhat bus station, actually from a parking lot in front of the bus station.
- Charyn Canyon is 50 km before Kegen. From the junction, it's about 12 km down a unpaved road with no public transport or taxis. Sometimes it is possible to hitch a hike with tourist vehicles, but often they are full.
- Continuing from Charyn Canoyn to Kegen: There is no other option than hitchhiking. It took me half an hour to find a truck which brought me there. There is quite a lot of traffic, and hitchhiking is usual in the area.
- Kegen to Karkara border: About 40 km, no shared taxis. A chartered taxi cost me 5.000 Tenge.
- Karkara border to Karakol/Yssyk-Kul: No public transport, the next village is very far away. The border guards offered me to call a taxi which would cost 60 USD. However, after 1 hour waiting time a passing car gave me a lift to Cholpon-Ata. There are very few passing cars, though.

Here is a detailed account on my blog:
https://passportparty.ch/2017/07/09/border-16/

With hitchhiking I mean: stand next to the road and putting your thumb up. I did it a lot in Canada and usually had a ride in 10 minutes.

But like I said, you have to be willing to do this. Some people find it, understandably, too risky. I never had any issues though. I am a 1.88m tall man, that probably helps.

So... are female drivers mostly willing to do it?
Haha!

You have the main options pretty much worked out.

For kyzart - getting there is very easy via mashrutka or hitchhiking from kochkor (anything heading west). You will be dropped off on the main road at the junction for kyzart. You then walk towards the little village of kyzart (10mins). Before you really reach the main village area you take a left turn and the guesthouses are all on that street (they are signposted at the turn, its pretty much impossible to miss). They can all arrange horses to take you up. If you don't want to hire horses its around 4 hours walk over Uzbek pass to song kul. I don't think the horse is actually that much faster. If you want to make a longer trek you can do as suggested above and go kyzart pass - kilemche - song kul - kyzart which is usually done over 3 days. I recommend doing 3 days but not going via kilemche and instead maximising your time at the lake itself:
Day 1. Travel to kyzart, hike/horse over Uzbek pass (4 hours).
Day 2. Explore the lake
Day 3. Hike/horse over Uzbek pass back to kyzart.Travel onwards.

If you go over Uzbek pass you can stay with any of the locals there (authentic yurt stay with real family as opposed to a yurt just for tourists). I can recommend musabek's family. If you decide to walk over the pass it is possible to hire a horse from the yurts for a small amount to explore the lake.