From a recent graduate class on Central Asia:

The boundaries were drawn up early in the existence of the USSR. From what I understood, the basic lines were drawn along ethnic lines, after Soviet ethnographers had traveled through the region. After this, Soviet officials from Central Asia began to realize that their home cities were going to be part of a republic that wasn't named after their ethnic group (A self-identifying Tajik realized his town was going to be part of Kyrgyzstan, for example). They lobbied for appropriate changes, and those were made.

This story wasn't part of any of the readings that we did for class, but was routinely mentioned by the professor. Hence the lack of detail, which I apologize for.

EDIT: More detail, from the ICG's report (http://www.crisisgroup.org/~/media/Files/asia/central-asia/Central%20Asia%20Border%20Disputes%20and%20Conflict%20Potential) on border issues in the region. While the borders may have been intended to be based on ethnicity, there were two complicating factors. First, the USSR worried much more about administrative and economic concerns, as these were administrative regions within a single country. Second, the political history of the region had created an incredibly complex ethnic landscape (and an uncertain one; the major ethnicities in the region all exist within several countries). This meant that any attention paid to ethnic boundaries a) took a backseat to administrative concerns, and b) was doomed from the start; no border could appropriately divide into ethnically pure countries.

Also, the ICG report calls attention to leases between the SSRs during the soviet period. These were similar to the granting of Crimea to the Ukrainian SSR that is in the news now. These further complicated the border situation, and gave credibility to the claims of folks that challenge the current borders.

Take a look at Google Earth and you can see how most of the borders were decided. The borders generally follow either topographical ridge lines or rivers which both tend to form well defined (sharp) and random (zig-zagging) borders.

Kyrgyzstan's borders generally follow mountain ridge lines except for the Ferghana valley which forms the tendril of Uzbekistan. Ferghana is ethnically Uzbek and allies culturally with Toshkent and the rest of Uzbekistan which is down hill of the valley's watershed.

The long straight border between Uzebkistan and Tajikistan runs between the river/watershed of the Amu-Darya River and the Zeravshan River. The two rivers have had separate cultural affinities as you would expect from the separation of desert between them. This has persisted to the current divide between the countries.