My copy of Breezebrowser can tag the JPGs but not the D800 NEFs, probably because I haven't bought an update license. But I kinda like using its hookup to Google Earth, so here's what I could do to copy location tags from JPG->NEF:
perl \ExifTool\exiftool -TagsFromFile ./gps/%f.JPG -GPS:all -r -ext NEF .
Would need to adapt this for a binary exiftool obviously. Also, the Lightroom tagger is nifty, but doesn't do altitude. Booo~!