To use DVD Shrink then the input needs to be a DVD-Video standard set of files (.IFO, .BUP and at least one .VOB file). Looks like you can set this up fairly easily from the original large MPEG2 file.
If you have VideoReDo already, then open the 6 GB file, select it all and save as ‘MPEG Elementary streams’. At the end of the save process, there’ll be two files, an ‘.mpa’ and an ‘mpv’ (audio and video streams respectively).
Next, download IFOedit from doom9 or videohelp.com. Fire it up and from the ‘DVD Author’ on the top menu, select ‘Author New DVD’. Add the two files from the VRD step above into the appropriate audio and video file boxes, and press ‘OK’. IFOedit will now make a DVD-Video compatible set of files, which you can now move into a ‘VIDEO_TS’ folder and open with DVD Shrink.