With that context, I think you really could jump in and do things on your own. Language can make things difficult, but not as difficult as you probably fear. The authorities you probably want to communicate with usually speak some English, while for those you don't want to communicate with (e.g., police looking for bribes) it's better to play the dumb tourists, anyway. Arranging transportation is where language is maybe the most problematic—especially since taxi drivers everywhere in the world try to rip you off—but it's not that difficult.
Visas can be a challenge, but they're not too difficult to pick up on the road, and lots of other people touring Central Asia will be in the same boat. If traveling East to West, you only have to get your Chinese visa at home (or in Hong Kong), and the rest can be picked up along the way (and it's easier now that Kyrgyzstan and Kazakhstan are visa-free). You'll meet lots of people lingering in Bishkek for visas. If you don't go to Bishkek or Kazakhstan, then you may need to get your Tajik visa and GBAO permit in advance.
In Kyrgyzstan and Tajikistan you can go through places like CBT, PECTA, and META to arrange homestay tours, either in advance or more ad-hoc once you arrive. In Uzbekistan you have no need of a tour to visit the big three of Khiva, Bukhara, and Samarkand, but local agencies can arrange for side-trips into the desert, to the Aral Sea, etc. There are plenty of agencies listed in Lonely Planet.
As for what you should see, I always recommend the
Silk Road Guide as a good starting place. It has lots of pictures and a more discerning viewpoint than Lonely Planet, and covers the Silk Road from China through to Turkey.
One thing I always tell people is that Xinjiang offers a more traditional Central Asian experience than pretty much any of the CIS 'stans. This may seem strange, but think of Turkestan as being a historical area that covered the area between the Caspian/Iran and Tibet/Gansu—an area which includes the 'stans and Xinjiang. But while the CIS 'stans have been under Russian and Soviet influence for well over 120 years, it's only in the last 20 years that China has become internally stable enough that it has been able to turn significant attention to Xinjiang: the current battle there between Uyghur and Han culture is a fight that was largely lost in the 'stans a long time ago. So I would be sure to spend some time in Xinjiang (not Urumqi, which has always been a Han town). I think the itinerary in the following thread is pretty interesting, even if only half of it is really related to the Silk Road:
http://caravanistan.com/forum/viewtopic.php?f=7&t=953
In Central Asia, I think the Pamir Highway and the Wakhan valley in Tajikistan are unmissable, and they offer a good mix of outdoor life, local culture, mountains, and stunning views with Silk Roads ruins.
Kyrgyzstan is geared more to outdoor excursions, yurt-stays, and horse treks, and less towards Silk Road sights (Tash Rabat, the Ozgen mausoleums, the Burana minaret near Bishkek, and maybe Suleiman Too in Osh are about it). The mountain scenery in Tajikistan is generally harsher than it is in Kyrgyzstan, which is famous for mountain pastures and horses (relatively few horses in Tajikistan).
Kazakhstan is much more expensive and modern than the other 'stans, and also has comparatively little to offer to visitors that can't be enjoyed elsewhere. Uzbekistan has the big three Silk Road cities, but compared to elsewhere in the region they are very touristy and people are more likely to treat you as a walking wallet.
Most people do Turkmenistan on a 5-day transit visa, which makes things difficult but even in that time frame it is possible to see the Darwaza fire-pit, as well as the sites at Konye Urgench and Merv (neither of which, in contrast to Uzbeki sites, are not horribly over-restored), with a brief stop in Ashgabat.
And for pretty much everyone who goes there, Iran ends up being a favourite—though the experience for females is quite different than it is for males, and unaccompanied females may be subject to harassment and chauvinism, though this is less likely if you're mainly in public spaces/cities (female cyclists seem to report it being more of a problem when they meet men in the middle of nowhere or while camping).
After Iran you can head straight to Turkey or do Azerbaijan, Armenia, and Georgia before going to Iran. I didn't have the time to visit them, but wish I did.
In my opinion, this would be a pretty much ideal itinerary after Kashgar (the bold are what I would consider essential, but I would also probably want at least one place from the Kyrgyz countryside, and one place from the Ferghana Valley):
- Torugart pass to Naryn, Kyrgyzstan, with stop in Tash Rabat (absolutely need a tour agency in Kashgar to arrange Torugart crossing)
- Song-Kul yurt-stay and horse trek
- Jeti-Oguz/Karakol
- cross into Kazakhstan at Karkara (need own transport or get lucky hitching)
- Charyn Canyon
- Almaty
- Astana by train
- Almaty
- Bishkek (get Tajik visa and GBAO permit while you wait)
- Arslanbob
- Osh, with a brief stop in Ozgen on way from Arslanbob
-
Pamir Highway to Murghab (best to hire car in Osh for entire segment between Osh and Khorog)
-
Wakhan valley
-
Khorog
- Dushanbe (apply for Turkmen visa for pickup in Tashkent or at Turkmen border, if possible; get Uzbek visa on the same day with LOI from Caravanistan or another agency)
- Fann Mountains & Penjikent
- Khojand
- Fergana/Margilan
- Tashkent
-
Bukhara by night train
-
Samarkand
-
Khiva by night train (only operates from Samarkand/Tashkent), with Elliq Kala tour
- Nukus if you want to see the Savitsky museum
- cross into Turkmenistan in early a.m., hire a taxi to Darwaza with a stop in Konye Urgench, and hike to Darwaza crater in middle of night for night and morning views.
- Ashgabat for a day or two
- Mary by night train, spend day in ancient Merv
- enter Iran
That is the basic outline of route that would be pretty amazing, I think. You could probably do all of this in a couple of months, plus the three weeks or a month in China. The cost for three months could be as low as the $4,000 tour you're looking at.
It would also be easy to cut off entire sections (such as going straight from Naryn/Song Kul to Arslanbob/Osh, in which case you'll need to have your Tajik visa and GBAO in advance).
There are a few segments above where you will need to arrange your own transportation, and this generally isn't a problem (either through an agency or simply arriving at the local taxi stand) so long as you're willing to pay. Things only become really problematic when trying to use share taxis or public transportation on less-frequented routes. As you were looking at a tour, I'm assuming it won't be much of a problem on the segments you need one.
Finally, as Steven notes, April and May is too early for the mountains, though good for the deserts of Uzbekistan and Turkmenistan.
