I had a similar issue in that I developed a lab assay, used it on one clinical study, modified it, used it for another clinical study, modified it again, used it for a 3rd clinical study. I wrote this up (Methods chapter) chronologically. Wouldn't you describe your questionnaire design in your methods chapter (questionnaire 1, subsequent development, questionnaire 2) and just have the questionnaire results in the results chapter?
NB I'm a quantitative researcher and have never dabbled with qualitative questionnaire type data so you might not want to listen to me on this one