Sounds to me like a couple of things happened.
First, I would guess that she thought "Shared Parenting" meant how time was to be divided and nothing more. In other words, her expectation was that she would be making all the decisions on the items you assumed you would have a say on.
Second, and possibly related to the first. Her attorney knows this stuff and probably saw the gap and explained it to her (either beforehand and thus her reaction) or afterwards if they had time to consult. Any good lawyer is going to get as much as they can for their client. Clearly, he (and the mother) were assuming control of the items you stated.
One thing interesting here and somewhat unrelated - notice how your gut twinged and your reaction - you spoke up before you signed away. There's a lot of sheep out there that just sit and feel their gut but say nothing.
I hope you guys can find a way through this.
Ironically, if you guys have equal time and given equal time the CS payments aren't outrageous, then the only control left is the choices you both assumed you'd be making. In a way, it's like whoever comes out ahead on this part of the settlement is the winner by a nose.
Maybe you could make a list of which decisions are the most important to you and be willing to give in on the others. For example, is a specific church that import (can't he just go to yours on your weekends). Maybe you get to pick the school and she picks the doctors, etc.
You could also bet that if she entertains that list it will come at some counter to give up something she was already willing to give up.
And you never know, maybe her folks or siblings told her in advance to the draw the line there and hope you wouldn't realize it.
If you can't reconcile this part quickly, follow the advice above and get a lawyer to make sure nothing else slips by.
