There is no program yet, though in theory, one could without too much difficulty write a script to just extract the filepos and proximate chapter headers in the unpacked mobi files and generate an NCX from that. And possibly this might be something Sigil could auto-generate from an ePub/HTML source, though I'm not familiar enough with that program to say for sure.
I do it manually for my own books which I mostly reconstruct and convert from ePub anyway and tweak the formatting along the way. I use a simple template in conjunction with a regexp which does most of the work for me.
Hope this helps and welcome to MobileRead!