Sounds like you're doing well. Working on organizing your life, I mean the room, is good stuff. You'll be surprised how things you change in the room might change things in your life.
When you stare at shelves full of stuff in fear, think of it as an opportunity to create a stage set. Have fun with it. Think about decorating a room with a pirate chest for spare blankets or stuff to free up closet space.
Discount stores are full of wicker baskets in many shapes and sizes that help organize in decorative ways. They aren't all girly. Some are darker and manly. As much so as baskets can be I suppose. I no longer have a desk with drawers. A work surface adjacent to a standing shelf tower works fine. The baskets on those shelves make it easy to see and grab all the things I used to have crammed into cavernous desk drawers. You can mix your own personal collectibles in among the shelf baskets. The largest basket on the floor gets all my paper recycle as I quickly fling through daily junk mail. It also helps hide the shredder behind it that gets the pre-approved credit cards and offers.
For a closet the same thing can work. Or, as others mention, clear plastic storage boxes and bins in different sizes let you see what was put in different containers. They get cheaper every day now. Of course if money is no object there is always the Elfa stuff at Container Store and RubberMaid copycat systems from Lowe's or Home Depot. Make the closet something you don't feel you have to hide behind a closed door. A manly dressing area!
Use this opportunity to express yourself. Use it to organize things in a way that will make it easy to stop future clutter from entering your life again. Make the bedroom a place you wouldn't mind hanging out in, even when she prefers to be in another room. Good for reading. Good for tv. Good window light. Try putting something at an angle. Maybe uplighting from behind a furniture piece. Consider mounting some floating shelves instead of nightstands, or above a dresser for extra storage and displaying family pictures.
Consider mentioning some of your ideas to her right before you do them, and let her know if the experiment doesn't work for both of you ... then you will study ways to improve on the first design. It gives her one chance to participate in a positive way if she wants to. Don't ask for or wait for permission to live your life. Not from someone who is not investing themself in it.
Keep making Jeff a priority and life a celebration.
