I think you have two options: 

1.) Normalize the tilt-corrected image to the raw (distorted) image and apply the transform to the processed images. Choose a normalization tool that allows you to apply a full affine (12 parameter model) transform (9 parameter transforms are insufficient, you are correcting for a shear). FSL's FLIRT would be an excellent tool for this. 

2.) Write a script that removes the shear from the tilt-corrected image. The function is described on these pages, as well as the dcm2niix code:

https://github.com/rordenlab/dcm2niix/is...

https://raw.githubusercontent.com/rorden...

float GNTtanPx = tan(gantryTiltDeg / (180/M_PI))/hdrIn.pixdim[2]; //tangent(degrees->radian)