go to Home Depot, Lowes or Costco and buy a bunch of the black plastic boxes with yellow lids and organize the parts into boxes as you take them off. take tons of pictures. i would also write a list of things you put into the boxes. you can organize the boxes how ever you see fit, but i suggest organization like exterior trim, interior trim, doors + windows, trunk, hood, brakes, lights, etc. then, when you buy new stuff, you put the new parts into the same organization.
i also recommend that you create bags that work with the orange book / real oem pages for all new bolts, nuts, washers + screws - keep the old ones and match the new ones as you replace them.