Writing two papers on two different topics with the same data = two protocols? I am a Ph.D. student and a member of a large interdisciplinary team of researchers working on a health related topic. We are shortly to commence data collection related to our topic of interest with a sample of around 250 participants. 

I have two very different research questions in mind that I would like to address with the same data set.  Q1) relates to the accuracy of the instruments used and Q2) to the association of our variable of interest with a range of psychosocial factors.

Being highly aware of the potential minefield that is salami slicing, I am being careful to be very transparent about my process. So I have written a protocol in which I set out both of the two questions and list all of the instruments collected. Consequently, I have had (entirely fair) feedback that this makes the protocol a bit incongruous and confused.

So, I'm wondering at this stage what I should do? Write two protocols, one for each question? Abandon Q2 and stick by a rule of one data set = one research question (this doesn't seem to me to be very efficient given the costs of doing research)? What of all the longitudinal data sets out there that have been used hundreds of times by different research groups? 

Would appreciate your advice, thanks!
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.