Red stems can occur naturally in some strains - I'm not familiar with these two but you can do a bit of research on it... other than that, red stems will indicate some stress is going on but, like - for example - a calcium deficiency will leave marks on leaves, even when you correct the deficiency, the leaves that are damaged won't be repaired... so some stems may just never go back to being the normal, good color. If the new stems that are coming on are a good color, I'd take that as a sign you've solved her problem... if they're all red, I'd look into the genetics.
As far as height is concerned, Blood Orange Haze may just be a smaller plant than the others or it may have been stunted - I would personally think she's just a smaller plant at this point. And even if she was stunted a little bit, I certainly wouldn't replace her - she can still give you a good harvest down the road.
Good luck...