Now is it enough to just convert the structures, or are there size problems
   with the structures on different architecures (different pack rules for
   alignment etc.) ?

   I can see a possible problem with 64 bit machines, or FFS clean enough on
   that score ?

The format of a FFS file system, except for byte order, is quite rigid.
If there *is* a variance between architectures, then it's almost
certainly a bug.

BTW, duplicating the entire file system is really not a proper answer
to byte-swapping.  There's no reason that a single copy can't detect
the byte order at mount time and byte-swap on read and write.  It might
be a tad slower (depending on the implementation details) in the
byte-swapped case, but that seems perfectly fair.