This sounds like a very big project. My response is to wash a load every day and deal with that load and then go on to something more rewarding. I'm not sure if your body responds negatively to touching the fabric or if you would get the same response to fabric stored in a stash. I keep most of mine in closed containers to keep them clean (no dust) and to protect from the light. If you store in closed containers you could wash just what you need for a project. Systematic approach to getting them the way you need them will allow you to continue to quilt. I do think we all need to be aware that fabrics do have chemicals that we need to deal with. I am always amazed at the amount of fabric stuff I find on my glasses every day as I work with fabric.