I think YABU and YANBU. I think you are getting a bit of a kicking, not entirely warranted as I think you're mostly just venting on here. I think when you have a bad relationship with your MIL, it can spill over.
YABU about your DDs not being flower-girls. Yes, it would have been nice and especially as you had the other little girl be a flower-girl at your wedding on your MIL request, but it is up to the bride and groom and they have chosen not to.
YANBU about some of the other things- I personally don't see the big deal about your DH being at your table instead of the top-table. I do think managing 3 children, 2 of whom are quite young and likely to be over-excited and tired by the time of the wedding breakfast, on your own might be tough (except for those whose children are an image of zen-like calm at all times, no matter what the situation) so I can understand why it might be nice to be with your DH for the meal. However, as it is not what the bride and groom want, I guess you just suck it up and put a smile on your face. Or don't go.
What she said about you foster son was utterly intolerable, and very cruel. She doesn't sound like a nice person TBH. That comment alone would have been enough for me not to see her again unless a heartfelt apology was forthcoming. And I can understand why you don't really want to go out of your way to keep her happy, when she is so unpleasant towards you.
That said, she is probably just not thinking about the impact of the plans (including last minute changes) on anyone else as she is concentrating on the wedding and/or is simply relaying messages not intending them to be seen as "instructions" that you are required to obey. She is probably not trying to annoy you, or anyone else. Though I can understand how galling it is when someone expects you or your family to do something they would not do for you (as in expects your Mother to drive to pick up DCs and look after them for the evening, when she wouldn't look after your DCs for your GMs funeral)- but that's not your BILs fault, so I think pick your battles.
If you really can't stand it, I'd be tempted to say to your DH that you'd rather not have the hassle and just don't go- but that you are happy for him to go and have fun with his family. Come down with an illness or something if you think it'd cause a major row if you decline the invite.