Fighter Factory won't do it. Fighter Factory will receive OpenBOR support (in fact, it alreay has on beta testing versions) but dunno if it will you let do this.
Anyway, you can use OpenBORstats for that, but the conversion isn't fully automatic, because OpenBOR and Mugen are different animals.
There are two ways to do this:
1- exporting all the images, with the proper axis. Open the character, go to sprites tab and choose "Save images (aligned)". It will save all the images aligned on the canvas and it will save a file with the proper axis.
2- Using OpenBORSTATS. Read the file "openBorStatsMug.txt" at OpenBORStats folder and follow the instructions.