I would like to setup an HTML vs Text version test to see which version has a higher click through rate.
Would I set this A/B test as a 'whole email' test and ensure both emails have only HTML or Text selected?
Whole emails is the one you want.
I would create the HTML email, and then create another email that is text only.
Then do whole emails test.
As Darrell mentioned, a 'whole email' test is the type of test you should create. We've done this test in the past, and although it will depend on the segment you are sending this email to, we realised that text emails tend to perform way better than visual emails as they seem to be much more personal.
Hope this helps you,