Fund space. I agree with Juliekcmo that the room should be set up to be the most functional and enjoyable for you for the 50 weeks a year that you occupy the space. I would put the couch in the alcove, and put either a sofa table behind it or hang a shelf on the wall behind it with brackets. That is the place for a lamp, a clock/radio/mp3 player, a place for someone to put a glass of water and a book at night. That also means that the window isn’t blocked so the room gets the benefit of max light all the time. Fan should move out into the room - do a cute chandy in the alcove, something fun and whimsical. The small chest that you have ready to paint seems like it would be the perfect companion piece for you to use for spreading out your files as you work. I think it would fit with the bookcase on the end wall to the left of the entry door to the room, based on the measurements you gave. Bookcase in the corner so that you can have clearance for the chest drawers once the armoire is on the other wall nearby. Then the armoire would go on the long wall, toward the bookcase and chest, to create the feel of an office area. It should still allow the computer to be visible for someone on the couch. To the left of the armoire, I would place the cute wood table you love, with a lamp. The tall mirror might work above this, to bounce some light around and feel anchored. Then angled in front of the stationary part of the french doors, your desk chair can be placed when you are not working. To the left of that, the little set of drawers, which seems perfect for CD storage, so that you can get them off the top of the armoire. You will then have a seating area for someone visiting if they don’t want to sit on the sleeper couch,(especially if it is opened), or you can sit and talk to your son in there while he is visiting. I would put the ottoman on the short wall to the left of the french doors, to get it out of the way when the bed is unmade or it isn’t being used with the couch. I would frame a grouping of the Audubon pix and place them on the wall by the closet. You could do a few more stacked over the ottoman. As for color, I know you said white, but I would think about a color that makes you happy to use in the workspace. I love the purple accent wall in the alcove, and if you still like it, that could be your other color throughout the space. Your pieces to be painted could be done in another (or the same) shade of purple. I could easily see green walls in there, something restful but deep enough to work with the large black pieces. I would paint the bookcase the the chest the same color if they are going to be next to one another, for a more cohesive feel. Consider something textural for the drapery and french doors, perhaps a textured linen or hopsack.

Creamy by Sherwin Williams will look great in there. It’s a nice cream that doesn’t read yellow. Or you can go with a white (extra White by SW or Chantilly Lace by BM). Sample it first, though. Buy a small sample and paint a large piece of foam core or Sheetrock, so you can move it around the room.

Do you have an elevation drawing of that stairwell in the living area? Seems the space under the stair landings could be better incorporated in your effort to locate the powder room, or at least the hot water, accessing from the closet by the entry and moving the sloset to the living room side. On another subject, am I mis-reading or are there bi-fold doors by the tub in the main bath? Looks like there are windows in the WIC. I would rather have windows in the bath and walk through the closet to get there than have to walk through the bath to retrieve clothing; not convenient if there is someone using the bath. That pantry at the foot of the stairs looks like a good spot for a stacking WD. I'd want it configured to vent out an exterior wall, using pullout pantries in the kitchen so that space could be the laundry. But first I'd move that big bath's footprint to the deck end of the space so the closet could be in the master.

You really need to find a home for all the books unless you use them all , all the time. Right now that room is no where I would like to sleep. IMO cover the fireplace with the murphy bed in fact you can even get one that incorporates an office . IMO this could be an office and a guest room and forget the den idea, Ilove books but IMO most info can now be found online and in a small space actual bookcases take up too much room this murphy allows some book storage a desk for you to work on and nice place for guests to sleep . Honestly in this small space I think that is all I would do. Or a sleeper and a desk maybe use a closet for other storage guests really require very small closet space