Central Asian history in general has been hamstrung by the fact that the region was under the rule of the Soviet Union for most of the twentieth century, meaning that until recently it has largely been inaccessible to Western researchers except through the lens of the oftentimes highly flawed Russian-language historiography. The Early Modern Period in particular (that is the time between the Timurids and Russians) has in addition been long neglected by scholars, largely because it's been written off as a period of decline. Decline is always a tricky concept, but in the Central Asian context it was seen as a process of political, economic, and cultural/intellectual stagnation resulting primarily from the discovery of new maritime trade routes between Europe and Asia, which supposedly brought to an end, or at least greatly diminished, the wealth passing through the region along the Silk Road.

Nowadays this view is being increasingly challenged, as historians shift away from a decline-centered perspective to one of transformation. Scott Levi in particular has pointed out that while activity along east-west trade routes may have diminished to some degree, this period also saw an increase in north-south trade, particularly coinciding with the rise of Russia and the appearance of Indian merchant communities in many of Central Asia's major trading centers. Much as in Ottoman historiography, the concept of decline is being overturned and replaced with more nuanced analysis. It's a slow process, but Early Modern Central Asia is becoming a more popular topic for research. Major works may be quite hard to come by unless you have access to a university library, but I can recommend the following as a starting point:

• Burton, Audrey. The Bukharans: A Dynastic, Diplomatic, and Commercial History, 1550–1702 (New York: St. Martin’s Press, 1997).
• McChesney, Robert. Central Asia: Foundations of Change (Princeton: Darwin Press, 1996).
• Levi, Scott. "India, Russia, and the Eighteenth-Century Transformation of the Central Asian Caravan Trade." Journal of the Economic and Social History of the Orient 42 (1999): 519-548.

Burton's book in particular is extremely detailed with regard to politics and trade, if you can find a copy it should be exactly what you're looking for. McChesney covers some of the conceptual issues one must tackle when addressing Central Asian history during this period.

For some selections from primary sources in English translation, see Levi, Scott C. and Ron Sela, eds. Islamic Central Asia: An Anthology of Historical Sources (Bloomington: Indiana University Press, 2010).