I've neglected to add a few things that should have been properly propagated from cutouts to measurements or calculated for the new measurements:
the coordinates should include the centroid offset for each measurement.
the badness bitflag that gets propagated from Image all the way down to Cutouts needs to also be propagated to measurements (and I've added a disqualifier cut that doesn't save Measurements that have a non zero bad flag).
PSF photometry: I've added this part using the new image's PSF (rather than the ZOGY PSF which isn't able to get sub-pixel shifted clips).
Forced photometry on cutouts: each measurement is able to give the photometry (in any aperture, or PSF) for any ra/dec that is close to the position of the cutouts. This doesn't replace needing to do forced photometry on images where there was no detection and thus no cutout.
I've neglected to add a few things that should have been properly propagated from cutouts to measurements or calculated for the new measurements: