I think I might just paint the paneling and save any extra dollars to add a big fat dormer for more windows and a little more headroom. Or perhaps to blow out a bigger window at the end(s). Making the existing windows bigger will not cost too much money. I think bed placement will be dictated by figuring out "if I sit straight up in bed, will I conk my head on the ceiling?" If you do conk, it will have to go against one end or the other with the higher ceiling, and then perhaps you could make the other end a sitting area. Dressers would work find against the walls with low ceilings.

Not sure of your style but I would definitely recommend painting the paneling unless you are a rustic kind of a person :-) If you lean more on the traditional side, you could certainly create raised molding on the lower half or paint the lower half of the wall a darker color for contrast. If you are a bright, bold and adventurous person, you could paint a vibrant color on the back wall with the window and put your bed there. You could put your bed on either side wall and create a ready nook with two chairs flanking the window on either side to create your sitting area. The opposite wall could then be used for low cabinets/shelves for storage of purses, shoes, etc..And without knowing what the other side of the room looks like, if height permits, they have fabulous free-standing closets at Ikea that might serve as your closet. Just some thoughts...