The jail image won't have enough stuff to boot as it is missing the boot loader, possible some drivers and maybe the disk partitioning. You can do an install of the same version on the standalone system, then copy over all the other files or look at the bsdinstall scripts in /usr/libexec/bsdinstall/. The auto gets run on a full install and it partitions the disk and installs the proper boot loader and asks more config questions. The bsdinstall jail does much less. If you compare auto and jail, its easy to see what you might need to fix up.
Have you considered building your standalone system as a jail host and run just one jail in it?