Welcome and hello
I'm sorry for what brings you here, and glad you found the site.
how can I start to set boundaries to protect myself and undo some of this action-reaction that I have fostered?
It's a really good question! Have you tried to set any boundaries already with her?
As you probably know all too well, people with BPD don't tend to have any boundaries, and many of us in BPD relationships tend to have weak boundaries.
In the act of learning to set firm boundaries, it's also important to learn communication skills to help with emotional arousal. Chances are, your wife is in a way retraumatizing herself through her relationships, sort of like an emotional limbo where she keeps creating the same dynamic with anyone in her intimate circles (including, it sounds like, your daughter )
If you have codependent tendencies, where your sense of self worth is tied to fixing/helping/rescuing, you will need to center yourself when the guilt comes up and floods you -- this tends to happen when we set boundaries. In many ways, this is the barrier that holds us back more than anything else. Change will be uncomfortable, and feel risky, and to make it even more challenging, she will likely escalate whatever behavior you are trying to protect yourself from, because she is testing the boundary to find the limit.
As an aside, asking your toddler daughter if she loves mommy and daddy, that is another area where you can practice your skills. It's inverting the parent-child relationship, where D3 is expected to provide the emotional support to mom, instead of the other way around. You can learn validation skills with your D3 as a practice run to get used to these small changes, and then work your way up to your wife if you suspect that too much change too soon will be tough for you.
LnL