You got great advice on building trust with your wife over time as you take your separate time.
So now I am at the point with my wife of how do i bring to her attention the BPD symptoms when we are going through it without me looking like I'm taking advantage of her situation.
My suggestion is don't bring BPD or symptoms to her attention. (Especially BPD. Many members have told a partner that they thought the partner had BPD, and good outcomes seem rare.)
Instead, focus on her behavior. When she behaves badly [driven by the BPD], deal with that.
Do what you need to do to protect yourself from the consequences of the behavior. Be consistent. She will fight/resist most likely, but will adjust, and everything will go better.
In addition, really try to understand if anything you do or say is invalidating, and try to eliminate that. The "good" thing here is that BPD makes your wife incredibly sensitive to it, and you will start to notice her (upset) reaction, which is often a cue that you just invalidated her.