I am looking for like-minded backpackers to join me. Depending on the number of people it can be done either independently (bus, shared taxi, hitching) or forming a tour group.
This is a beautiful route usually only possible during the season. What is more the Shepherd's Festival (end of August, near Char-Kuduk in Kyrgyzstan) is just around the corner. Will make a stop at Charyn Canyon on the way from Almaty to Kegen.
I should make it to Almaty by 27 Aug. Send me a PM if you are interested.
From the OP (this is how I did it):-
Took 13.30h marshrutka (150 som) from Karakol's Ak-Tilek Bazzar's SE side towards Char-Kuduk. Got off at junction and trekked to the border (about 5-6km). As the marshrutka was quite slow we reached the border after it was closed at 18.00h. You can camp by the border or hire a bed at the 'stationary train carriage' there. You need to bring your own food and water.
Next day crossed the border and walked 13km to the next village Kapkapa to catch a taxi to Kegen.
It was early September, for some reasons there were significantly more south-bound traffic than north-bound so our hitching opportunities were not great. From 08.30h to 13.00h that day we saw 3 north-bound vehicles (cars and jeeps, no trucks) and none stopped for us.
There are frequent fast shared taxi from Karakol to San Tash village at 100 som.