Dear Dr. Dhollander,
Thank you so much for your detailed response. That is a relief about the mtnormalise function, as one of my advisors was asking about this to me, so now I can tell them 
Ah, it makes sense to use the dwi2response dhollander instead of the dwi2response msmt_5tt to estimate the response functions for my data. For some reason, I had thought that the dwi2response msmt_5tt was ‘better’ and more accurate in the sense that it utlilised more mri data, but I was wrong about that! 
Following the mrtrix manual, I would then use dwi2fod msmt_csd since I have multiple shells (b0, b1000, b2000). Since I do have other mri data (e.g. t1w, t2 FLAIR), I was wondering if I could still use these in my analysis? Such as, would it be appropriate to still create the 5 Tissue Type Image and use it as a tissue constrain in the tractography generation (i.e. Anatomically-Constrained Tractography (ACT) in tckgen -act image)? One of the reasons that I did not do this initially was that I read in another mrtrix community forum post here that the combination of multi-tissue CSD and ACT may not be appropriate.
Thanks,
-Lenore