No, you do not want to run 3dWarp to deoblique or oblique. That will apply another transformation. If you want to get rid of the warnings, you can run "3drefit -deoblique" on any dataset that triggers the warning, but you remove the obliquity information from the header, so you may want to do that from a copy; or you can set AFNI_NO_OBLIQUE_WARNING to YES in your .afnirc file.

The -tpattern seqplus option you provide gives 3dTshift enough information to generate your intended output. By providing the options with the various "_opts" parameters, you override the default ones, and that may or may not be something you want. For example, the tshift_opts is usually "-cubic". By replacing that option, 3dTshift will uses its default of Fourier interpolation. For the purpose of aligning the anat to the epi dataset, this will probably not matter, just something to keep in mind.