Thanks decoenthuasiaste! I think we will follow your advice and position the desk that way. This way I'll have the window to my left and can look into the backyard if I want, and also face the large wall where we can place a nice long & short bookcase with art. I think the reading area to my right (on wall that current has guitar and standing lamp) will look great. We are going to try a rug like this one to complement the more modern bamboo desk top and dark navy walls:

Here's what I might try: Obtain a L-shaped desk with a right-hand return. Position the return along the window wall to the right of the window. The desk extends away from the window wall towards the closet (when sitting at the desk you look to your right to look out the window). Allow some space between the return and the adjacent walls to eliminate the impression that the furniture is jammed into the corner of the room. Check if the "cable box" can be mounted vertically. If so, attach a piece of painted wood to the window wall and hang the cable box on it. You don't want to set the cable box on the desk. Unless the computer is enormous, obtain a bracket and hang the computer underneath the return. Position the computer so you will not bump with your knees it when sitting at the return or desk, or switching between them. Attach cable guides to the underside of the desk and return to keep wires off the floor. Optionally attach a keyboard tray underneath the return. Obtain a table for the printer and position it under the window to avoid putting the printer on the desk. If the printer must go on the desk, put it in the corner near the window. If there's space, put some shelves along the wall between the window and the closet. If not, hang some shelves or cabinets over the return to the right of the window. Optionally change the closet door to a folding door so it doesn't project so much into the room. If there's space above the safe, attach some shelves or cabinets there. -- amateur

I am not a fan of the backwards books, as I feel that it removes all functionality. While design is important, good design should also be functional (IMO). However, I don’t see anything wrong with sorting the books by color, that‘s both functional and can look interesting. If it was me, and I wanted to color code, I would do small groupings of the same color on each shelf (rather than a single color per shelf) and mix in photos, plants, and decorative objects. I also like how Marta’s shelves look in the post above!

Following up my earlier comment…if you pull the cubby into the middle of the space as a partition, there are lots of options for the desk…on the dark wall (monitors/wires will disappear/blend in); facing the back of the cubby (which could be trimmed out/painted/wall papered/decorated or covered in cork as someone suggested; or perpendicular to the cubby partition, especially if there is a window with a view on the wall we don’t see in your photos. Don’t worry about the monitors…arrange your desk in the position that feels most comfortable for you while you are working. The mudroom cubby area should be on the side closest to the door into the room, which I’m guessing is on the right since that is where you placed the cubbies. The good thing is you can move/tweak the placement of your desk and the cubbies until it feels just right for you! I would anchor the office space with a rug and place the chairs and the mirror (vertically) in the cubby space. You could do a gallery wall on the dark wall. I think it has a lot of potential and makes good use of the room!