Writing two papers on two different topics with the same data = two protocols?
Data sets can, should and are used many times over. Your two very different research questions appear to be candidates for two different research papers, since the one is methodological (instrument accuracy) the other is not. 

Even if you keep them very separate in your protocol, lumping them together in one document may indeed be detrimental.

It also appears to me that the methodological question should be worked out first, since the conclusions/findings from this front will qualify positively or negartively the findings related to the other question.