I’ll mark this as solved, thank you!
Below is the same run 28 T2starmap.nii.gz as before, but left is when the last 9 (3 * 3 noise scans) .dcm files were deleted from the dicom directory prior to running dmc2niix. (I confirmed that all three echo’s BIDS .nii.gz had brains in all frames, and then ran fmriprep as before.) The combined output timeseries also looks much better - no stripes.
I’ll be running more tests and plan to share details on my blog as they develop. We may indeed try NORDIC or other denoising in the future, but this (hopefully) will be a starting point.