Your questions are too vague to answer, and you don't give enough information about your planned analyses to provide any advice.

What do you mean by "voxel-wise analyses"? That's pretty much all that the standard AFNI programs do, and they do the preprocessing steps that you mention. Where did you hear "that in voxel-wise processing some of these preprocessing should not be done"?

In fact, the subject of preprocessing FMRI is not a settled area of knowledge, despite 20+ years of experience. There are significant differences between the way AFNI, SPM, and FSL preprocess time series datasets. In some cases, these differences affect the final results fairly substantially.