Help with forced ranking

Hello,

I'm attempting to use OmniGraffle Pro (latest version) for a project
that I have been working on to build an "orgchart"-style genealogy
list of every named character in the bible. Yes, I am all sorts of
crazy. (But in the nice, geeky way.) Unfortunately as I've reached
>1000 objects (and still working on the Book of Numbers), I'm
increasingly running into difficulties ranking the boxes and it's to
the point that I just want to throw it all out and start over on
another tool... but as that would be a real waste, I'm hoping someone
here can tell me how I should do this differently.

You can see what I'm up to here
(http://coatofmanycolors.net/2010/11/28/exodus-complete-genealogy/),
but I can also provide a .graffle file if that helps. My local copy is
much farther along than this.

As I get into the later books, I need to make sure that I am ranking
the figures in the correct row based on approximately where in the
story the characters appear. So, a new figure would not appear at row
1 ("God"), but rather in the same row as Moses, if he happens to be
around at the same time as Moses.

I have been accomplishing this by selecting the one that I need to
move down and an item in the same row, and using the "Selected Object
Rank" -> "Same Rank" feature. This seemed to have been working for me
for a while, witha  few hiccups because sometimes it would make the
wrong one go *up* instead of the right one go *down*, but it seemed
that if I selected the right one second that it would work out.

The problem is that I'm getting to a point where when I do this trick
and move a figure down to the right row, it often forgets another one
and he or she moves to the wrong place. This could have been happening
for a while but as you can imagine this error is a pain to detect. It
would be GREAT if I could set the rank numerically, but I don't see a
way to do this. Is there another way to accomplish what I am trying?

As a side note, I'm finding that I have to be pretty careful and have
to once in a whole revert to a save because it screws up somehow and
makes some boxes 1 pixel tall or other weird glitches. There are also
some annoying-by-fine cases where the subgraphs end up aligned weird,
like having lines cross when it really isn't necessary. But those can
be dealt with if I could figure out how to ensure (without turning off
auto-layout which has been a godsend, so to speak) the forced-ranking
problem.

Thanks for any help you can provide. Let me know if anyone has tried
anything like this before and have a better strategy.

Joe