FanFiltration said:

I want to use the DVD set as the source master, but the theatrical versions are anamorphic 16:9 and the deleted and extra scenes are all full frame open matte. I could try and create letterbox versions of the deleted and extra scenes, but that would mess up the sub-titles that would be cropped over. So new sub-titles would have to be made to match the rest of the film, and done in a way to cover up any of the original ones that may still show after cropping.

You don't have to crop the exact centre of the frame. You could (and with cropping 4:3 to widescreen, that's usually the better choice anyway) leave more of the upper part of the frame and less of the bottom, thus covering the subs altogether.