In our database, we have question versioning and option versioning. For example, in wave after wave of survey administration, a question make go through several versions and be incremented up each time. The responses are tied to whichever version was used. Is there a way to indicate that within Qualtrics so that it can later be utilized when pulled down from the API or even a regular download?

If I understand you correctly, you can use Embedded Data for this. You can pass the version through the URL.

Metadata - does it exist | Experience Community