Hi,
Regarding 1, yes, you will need to register your fMRI and diffusion data. There are multiple ways to do this. I’d register the first volume or an average across (a subset of) volumes of the fMRI data to the average b0. This gives you transformations that you can apply to your ROIs and/or the images to perform your analysis in either space. If you need nonlinear transformations, have a look here. Otherwise there is more information for instance here or here.