And watch out for pathgridding. It's a royal pain.
It can't be worse than Navmeshing for FO3. I've messed with it a little, and it's pretty straightforward, though tedious as hell. I only tamper with the vanilla worldspace when absolutely necessary (adding a tent outside Gottlesfont or an additional cavern, for example). I prefer to make my own worldspaces to screw up.
I pay pretty close attention to the AI package conditions (I tend to rely on variables more than stages), but I'm sure any discrepancies will be discovered in testing.
The prologue is roughly 15-20% done, all things considered.
Thanks for the info and suggestions - I'll keep you posted.