This all seems sensible – though as always, it really depends on what your research question is exactly, etc.
The only thing I would query are the two mrtransform steps in your “1 Convert DWI to mif” stage: there is no reason to do this as far as MRtrix is concerned. You can keep the T1 and the DWI at their native resolutions, and use any derived outputs (e.g. the 5TT image) with tckgen alongside the FOD image derived from the DWI at whatever resolution that was, and provide ROIs derived from a different image again (maybe that’s what your registration to MNI is really about?), and it should all work correctly. These images can be coregistered even if they are not on the same voxel grid.
More to the point, the mrtransform commands as you have them will just regrid the data onto a voxel grid to match the MNI template, but they won’t actually perform any coregistration as such. This will only work if the images are already coregistered. I recommend you have a read through @maxpietsch’s excellent wiki article on the topic if any of this is unclear.