A very intersting idea, hehe... Good luck on the full presentation of it... Now here is my little 2 cents...
Where did you pick up the idea that they have something like a Combat Cassandra's Tears? I'm not sure if they showed anything more than a huge number of skills due to being as old and active as they normally are... But I guess I could be wrong on that, hehe...
As far as the regeneration goes, maybe do something along the lines of they can regenerate along the lines of the red stones they used to keep themselves alive... Maybe ever person that is thus "used", turns into a single stone, or maybe every increment of people provide enough to attempt one. Then you also get into the idea of that while they may be creatures made my magic, they are completely unable to use it themselves, thus have to find promising individuals that they may teach some lesser form of Ritual to, in order for them to try to reach some goal they want *shrug* I know I'm ripping horribly from FMA now >.< Feel awkward doing that, hehe...
But it was just as an idea, so you can have an idea of a set amount of times Mythic Regeneration can bring them back "from the dead" and such. Maybe keep track of the total amount of Stones each of your villains has attributed to themselves, and that their total regeneration comes from the stones. So if each stone is worth a mortal life, then each stone then has a total value of about... 20 shifts worth of consequences, maybe more depending... But that would be a good possible place... A little bit more definitive then just 100 lives, and also more manageable for the PC's in general, hehe... Just a bit more difficult on paperwork
The only other thing, is while I understand the Catch of Thaumaturgy, I think its a little too difficult of one to be used in combat.. Thaumaturgy similar to the way Ed used Alchemy just really isn't doable, unless the individual has Sponsored Magic, and even then, it would have to be a particular kind of Sponsor in order to get the kind of Thaumaturgy you'd need... Maybe some form of Earth Evocation Catch, where the individual has to basically "make an attack on the very physical make up" of the homonculus, IE place a maneuver on him, that they need to tag the NEXT exchange, before the effects go away. I'd also think of giving him Supernatural Toughness as well, with the same catch. Thus, if I'm getting this right, It'll turn into Inhuman Toughness once the catch is used. I only state this, cause Greed in particular was a bitch to kill, and even after the catch was achieved, he had SOME level of toughness left to him...