So I'm getting close to where I can start planning how the loading routine will work - after how quickly all the rest of this went, that's kind of disappointing to say, but what can ya do?
The way it's going to work is this:
There will only be 14 actors - DkC, Kain, CRy, Tellah, Ed, Rosa, Yang, Pal, Por, PC, Cid, TRy, Edge, FuSoYa - but there will be room for Golbez and Anna if anyone ever figures out how to make them fully functional. That is to say, there is no Kain 2, Tellah 2, etc.
When an event instructs the game to load an actor, the game will first look into the Shadow to see if the character is being stored there (every character has his or her own slot). If there is no shadow data for that actor, then the game will run the initial stat loading routine (which will be essentially unchanged).
If there IS relevant Shadow data, then the game will load that, then will load the five character-dependent stat bytes (ID, job, crit%, crit bonus, steal evade) from a custom table. Then the game will run the level-up routine, since exp is stored in the shadow but level gains are not performed there.

Rydia will be the exception to the process. Teen Rydia will load only from the Shadow (has no initial stats), but will have a unique entry in the five-byte table. Child Rydia will load either from intial stats or the shadow, like any other character would, but it would only be wise to load one or the other at a time. If Teen Rydia is in the party, and Child Rydia is added, then Child Rydia will load from initial stats (because Teen's load would have cleared the shadow). In that case, if Teen is removed from the party, her stats wouldbe stored in teh shadow. If Child was removed from the party after that (but before Teen was loaded back in), then Child's (presumably lower) stats would overwrite Teen's shadowed stats... does that make sense?
That
should work. Although TNLs don't work exactly as I thought, I don't think, so I might have to throw in some extra calculations. I keep saying I'll cross that bridge when I come to it...