Ugh, My advice probably wont help much, but here it is from the point of view of the ex's wife....
Oh yes, she will be jealous you are pregnant, not only do you have the ultimate relationship with the kids she is trying to be a family with, but youve gone and got yourself another baby that you dont have to share! It may not sound rational, but its very hard when you cant have kids of your own. It hurts, alot. Give her a break with that one, ride the resentment. Nothing you can do about it, she actually probably IS crying every night. While still an overbearing Stepmother, she is still human.
As for her stepping over the boundaries... Wow... I would have LOVED to overstep my boundaries on several occassions (probably did, unawares), but really tried hard not too. From her pov, these kids of yours are her only family. Who CARES if she tries to be a good person to them? Her motives may be in the right place, they may be in the wrong place, but its a hard one to judge. You are both battling over ownership of very separate families when you dont need too. You, as mother, (and saying this as a hurting steppie) will always be Mom. The more you let natural relationships lie, the better it is for the kids, even if you end up crying every night doing so.
Try your hardest to find empathy for the woman who wont be able to rub her tummy like you can, talking to her soon-to-born child. I know it doesnt seem fair, or right, and you probably wish at times that she would *&*( OFF!
That aside, feel pride for yourself, youve put up with more than many mothers could or want to contend with, and dont give up. I never thought my relationship with biomom would get to the place where I can call her just to yak, and I doubt thats normal to be honest, but keep persevering if you can find the strength to do so, do all the school stuff anyway, she is obviously trying for whatever reason - once you find empathy in your heart, youd be surprised what happens afterwards. Even a coffee for her might change the way things are, with no expectations of a thanks. She might just throw it out, throw in your face, you might not WANT to do this, you might think.. well... whatever. But life will be easier once civillity starts, and unfortunately someone has to keep making the first steps over and over till the other one breaks.
Good luck, you sound like such a devoted mother who loves her kids with all her heart, and you CAN do this, you so can put it aside and be the bigger person, you can be there at school for the kids and trust me - I will always love my mother for dealing with my step mom the way she did. She was amazing, and you will never be forgotten by the children for being so damn awesome through a really hard situation!