After I received an email from RedBull, I spoke with several tenured and t-t faculty to get their opinions on how to deal with this.

Based on their advice, I answered her email with one that said I value our relationship and have absolutely no intention of stepping on her toes (And really this is true) .  That I respected her preliminary data collection and thinking for this system.  My only interest was to find a niche in an area that will take advantage of my expertise.  As I didin't have a clear understanding of what she was proposing, I didn't have an appreciation for the overlap the way she did.  I then asked her if she could help identify those specific areas and questions where she thought there was overlap.  The email mentions my surprise at her email because at the time I was offered the postdoctoral job, one of my criteria for taking the position was that the PI, that is her, was willing to share the system (and she was during the interview).  I further added that it was my recollection that we had an additional conversation at a conference earlier this year where we talked about me using the system to answer questions that spoke to my expertise.  I ended the email by saying how much I appreciated her investment in my future and that I thought we had a lot to work out in terms of how I might acheive a thriving and complementary, yet independent research program.  Once she delineated areas and questions that she didn't want me to work on I would be happy to step back and let her pursue those aspects.

I didn't address her specific comment in the email where she says,

 "I understand your desire to put your best foot forward in your research statement, but I am still concerned that you have not made a clear distinction between your research accomplishments and my research program."

It was my impression that if you said you were doing the work as a postdoc in such and such's lab - it was implicit that it was part of the PI's research program? 

One of my faculty friends suggested that given this issue, it would be a good idea if I sent her an email saying that because we still need to work out the specifics of overlap and that this is unlikely to happen before job apps are due, can she write me an unambiguous and enthusiastic letter of recommendation.  So I sent her an email late-afternoon Monday.  Guess what, nothing.  Not only that, I saw her at lab meeting yesterday (tues).  Not a word about letters of reference.  So I followed up with an email that said, I realize you're super busy but these applications are due in a few days, perhaps you'll let me know one way or another so that if I need to, I can find an alternate letter of reference. 

This is where the "super wow" comes in.   I have still haven't heard and based on this lack of response, I'll assume her passive-aggresive answer is, no.   Of course, I'm not stupid and yesterday morning I sent off two emails to people I've worked with to see if they'll be able to write me a letter. 

In the end, she has completely shot herself in the foot.  I say this because with an NSF renewal coming up, she is expecting me to work my ass off for her to get two papers submitted.  But if I can't ever count on her to write me a positive letter of reference, then really what power does she hold over me?  None.  

In the end, what I should do is work on manuscripts that will benefit my future and establish me as a thriving and independent researcher.