I'm particularly interested in the time in between the collapse of the mongolian empire and the expansion of the russian empire into the region
There's not a ton of (English-langugage) scholarship in the region, but when I traveled there I asked the same question here. The UN History of Civilizations of Central Asia was a consensus choice, and is free to read -- you can download the PDFs here. You probably want volumes 4 and 5, or at least the latter half of volume 4.