you've posted this 3 times. please delete the other two before someone comments on it.

Thanks. First time and it kept saying they didn't post. Now I am trying to figure out how to delete.

Hi looks like you have a couple options, yes you are right staining the floor darker will hide any of the lighter stains you currently have on the floor for the most part, the darker you go the more will hide.., 2nd the boards can also be replaced that are stained and will match perfect after job is sanded and finished if you choose, However it can start to raise the cost heavily in replacing individual boards. We have also have tried taking just a few boards out in a larger stained areas randomly to break up the stained area with new boards which kept the cost to a price the homeowner was satisfied with. I love you the old pine floor ! with the room separation I don't see any problem with the transition! is of course personal preference as you will have to live there! You can stain the oak closer to the pine for a smoother transition, if you plan to sand the entire area have your professional give you a sample of what the finished products will achieve and you can choose your colors then. Good luck ! congrats on the new houzz!

These 2 woods will take the stain differently but IMO i f you use the same stain on both that will be the best choice and if you need to use the darker than do it