Well, it looks as though you have gotten yourself stuck in a somewhat precarious position. Just do the experiments, don't let anyone except Big Boss Man know what you are doing, write the paper and let him decide what he wants to do with it. Isn't that why they pay him the big bucks (and he pays you to do what you are good at?) At this point, is it really worth arguing with research scientist about her data, her manuscript-that of course just needs tweaking-and how this is going to be her paper submitted this year. It is not worth it. You've already talked to Big Boss Man, he told you what he wants you to do (and of course your really cool experiments that go with it) and knows that the research scientist is not happy with this arrangement. It's not your fault the data is shitty and needs to be redone. It's not your fault you know how to use really cool technique. Suck it up, shut your mouth and don't get baited into an argument with research scientist about it.
Dear Research Scientist-
First of all, thank you for giving me a copy of the paper you are working on. No, wait, you didn't. Big Boss Man had to photocopy it for me. Ok, let's start this again, thank you so much for including me in the author list of the paper you are writing, especially since you go into details in the methods about the really cool experiment that I have researched and I am going to run. Oh, wait, that's right I wasn't included on your author list. Hmmm...ok thank you for arguing with our boss about where to submit the paper- I do agree that our normal, default (but still very good) journal may not be the best place for this paper and commenting on how long it is going to take me to do everything so we just should submit the incomplete, preliminary data to highly competitive journal and look like a bunch of idiots. No, that one is genuine, you did do that. Thank you for throwing me under the bus, trying to make me look like an idiot with no skills.
Time will tell, dear research scientist, time will tell. And oh yeah, shooting to get out one paper every two years- not so much. You are lucky Big Boss Man is cool and has already established himself-where else can you go where a paper (or short communications) is productive enough (average for our field-dear one- is 1-2 papers every YEAR). But, I know you are busy and supposedly make less money than me (because you pay daycare- that makes no sense in my brain). Really, I must thank you though for bringing out the attitude in me, bringing back the drive and the constant pressure of trying to prove myself. Thank you for not making the lab a motherfucking care bear tea party. I appreciate the competition. Bring it on. Please do not feel bad if I ignore you in lab. I do not want to hear about "tummy" aches or anything else you have to say. Its not personal, its business. Wait, no it is personal...never mind.