I think she is a touchy/spirited baby, she certainly shows some signs of spirited, but like you say only now are we beginning to understand her more and she gets less frustrated with us, and vice versa, as we can interpret and intercept things before they become huge cries usually. Her worst cries come when she is tired and we cant get her to sleep.
I have to be honest coming across the visual stimulation thing was pure accident, and I put that incident and the other issues she has together, and began thinking it might be that, certainly in the car at night she hates it, the lights pop up in front of her and make her cross.
We are fortunate that the nursery is cream with pale pink, so when we get her in there that will help, although again pure luck!! Good idea to remove all toys and stimulation from there though.
Phoebe likes you shaking toys occasionally but only specific ones, and she gets fed up quickly with those, she much prefers her changing mat mobile (if you can get one it has worked wonders for Phoebe, she sits and coos/smiles madly at it!)
We have a black out blind for her room (again when we get her in there), and she already has one of those sleep bags, which does seem to help her, again we dont use that during the day though, so something to consider for those daytime naps...