Use this information as a helpful datapoint, but of course keep in mind that your experience and conditions may vary!
Please note, second half of September is the very end, or past the season for this hike. I thought it'd be useful to explain what the conditions were like at that time; read on!
Hike difficulty. The trail offered no major technical difficulties for an experienced hiker. For example, I only felt the need to use my hands once, at the start of descent from the the Sary-Mogol pass (it was slippery and steep). However, we did have to walk in snowy, low-visibility conditions for hours up to Jiptik Pass on the fifth day. Overall, this hike definitely requires some mountain experience and decent fitness.
With our heavy backpacks, we would not have been able to compress the hike comfortably into fewer than 6 days. For calibration purposes - we're both reasonably fit, having both run either a 30k trail run, or a road marathon this year.
The trail is not marked. Most of the time it's very clear, but sometimes you encounter trail splits, where it's not clear which one would be the one to follow. You will need to have a map of the trail and navigate.
Before starting the hike, we stayed one day and night in Sary-Mogol (3000m) to acclimatise. I experienced mild headache from the altitude during the first camp night at 3500m, and breathing was strenuous when walking up to Sary-Mogol pass (4300m) on day 2. After that, no more problems. Your mileage may vary, of course!
Options for modifying the route. We walked exactly the loop that AllTrails shows, but we learned that you can get a ride to cut roughly the first and last 16km of the hike, which would have made it two days shorter at our pace. I would definitely recommend the walk though, because most of it is really beautiful! It's not like you're walking along an ugly busy road.
We also heard from another hiker, that instead of doing a loop, you can keep hiking north and hike all the way to Osh.Water. We carried 2L of volume each, and had a water filter and chemical treatment tablets. The entire hike follows streams, which makes this approach possible. There were some segments were there was nowhere to get water, because the stream was dried out, or not accessible from a part of the trail, but overall we never had concerns about sourcing water in time. The water in the streams was clear, except on the way to Sary-Mogol pass, where something was colouring it yellow.
Other hikers and yurt situation. There were very few tourists on the trail. We were aware of another group of hikers a day ahead of us (met one of them at the Osh airport earlier), and we walked the hike at the same time as two other hikers, who stayed in yurts. A lot of the yurt camps marked on maps (e.g. Strava) were already wrapped up for the season (simply not there anymore), but a few were still operarting and taking tourists. A few of them gave us water; it may have been taken straight from the stream, so you may want to filter and treat it regardless.
On the 24th, we met hikers just starting the hike (in the opposite direction), who also said they have yurts confirmed. The weather was not very nice, but they were hoping the forecasted sun would melt some snow and raise the temps up. Hope it went well!
To be very clear, you should arrange the yurts ahead of your hike, if you plan to stay in them!
Language and people. The locals we encountered in the mountains, and most people in Sary-Mogol (with exception of our hostel host) generally did not speak English. We communicated using a few Russian words we knew, or a translator app. Everyone we met was friendly and used to tourists.
Weather - rain and snow. Our first 3 days were clear, without rain; maybe some drizzle at night. We literally only stepped on a small patch of snow once at the Sary-Mogol Pass (highest point of the trek, day 2).
On the afternoon of the fourth day there was a downpour coming down the valley. We sheltered under a tree for a bit and the weather cleared up.
On the fifth day, at around 3500m, it started snowing, and around 20cm of snow fell, as we were getting up the Jiptik pass. We ascended in snowfall and low visibility. We are optimistic that the GPX would have been good enough to find a reasonably good way up, but it'd have not been easy. Luckily, we had footsteps of the hikers in front of us to follow. On the way down from the pass, it cleared up, and we exited snow level at around 3400m. We camped at 3300m (no snow there, when we went to sleep) and woke up snowed over. On the last day, snow ended at around 3200m. It was raining very cold rain as we entered Sary-Mogol.
Weather - temperature. We spent a majority of the time hiking in two layers, or one. At the lower points of the hike (at around 2300/2400m), when the sun came out, it was properly hot. I spent the nights (we always slept between 3000m and 3500m) wearing two top layers, one bottom layer, and a warm beanie, in my comfort 5C sleeping bag, and I was warm.
Animals. We did not see any dangerous animals. We also did not get close to any unaccompanied dogs, except one guarding a house on the last day, as we were exiting the valley, walking down to Sary-Mogol. I suspect you may encounter more dogs earlier in the summer, when more farm animals are up in the mountains, but I'm not sure.
I would recommend you seek local advice about whether carrying bear spray is recommended, and make your own decision.
We saw a lot of yaks, some of them walking very close to us. They mostly didn't seem interested. Sometimes they stopped and stared, and when we said 'hi' to them, they'd start moving on. Once we had to walk through a large group of yaks (there was no other way), and moving slowly, we walked through without them paying any attention. Overall they're huge and have big horns but they don't seem to be a concern.
There was also the odd random donkey, lots of cows, and lots of horses. Every now and then, shepherds would be leading sheep along the trail, and you'd have to give way.
We saw big orange marmots one of the days, but they hid before we got too close. We also saw a lot of big birds of prey in the sky on multiple occasions.
On the last night, some mice crawled out of a hole near our tent (we could see the footsteps in the snow) and looked through our belongings... Beware!
Getting there.
There seem to be no good hotel options near the airport at all! We stayed centrally, which was about 30 minutes ride on the empty streets at night.
The small 'Rysbek' store was the nearest store to our hostel and we were able to find some snacks there. The store is a bit hidden away from the larger street! There was also a couple other larger stores, including along the main road. There was a food place along the main road too, but nobody was inside when we came by. Likely that's because it was Thursday, which is apparently the market day, and a lot of people were gathered at a location along the main road, selling and buying stuff.
We fully relied on our hostel/guesthouse for meals; they served good breakfast, lunch, and dinner, at request.
Camping stove gas. Our accommodation in Osh happened to be selling camping stove gas. If you need help finding where to buy some, I would recommend messaging Visit Alay ahead of time.