I've spent days and days trying to figure out the way FrameMaker handles cross-references. I am not surprised at all that you cannot simply edit the MIF file and make it work. Are there good reasons why you need to handle this in the MIF files instead of using ExtendScript to do it on the FM files from within FrameMaker ?
Check my FrameScript tutorial on cross-references at http://www.frameexpert.com/tutorials/cross-references.htm. The code is in FrameScript, but the concepts will be the same with ExtendScript. You can insert and manipulate cross-references directly with FrameScript or ExtendScript without having to use MIF snippets.