Hmm, I'm not sure how well the in-game shadows work, but could you just get a normal day-night cycle going, then build the cave double-sided so the outside blocks the light? As in placing big block pieces to sort of box in the cave except for the opening where the light would shine down.
I've never tried anything like that so I'm not sure how it would handle it.
Likewise, you may be able to have a "simulated" effect, if the sunlight doesn't work, by using a gigantic "light" that you would normally use to light interiors. Then scripting it to turn off at night. Not sure what you would do about skies, but I think you could do a similar thing with simulated skyboxes that switch depending on the time of day. No way to make anything fade smoothly with scripting though, so getting natural sunlight to work would be [censored].
As for assigning cells different weathers, (I'm not sure what sub-cells are exactly), I know you can do that and they won't bleed over.
Sounds like an awesome idea though, will have to post screenies of your progress!
And thanks much by the way. What was the You-Tai-Thingy area you mentioned? Sounds fun