I tried once to work with wire and beads with ordinary needle nosed pliers. It might have been my inexperience but it was a complete disaster. I think the plier tool is one thing I would put on your must have list.
As far as organizers and storage I work off of a plate because I hate trying to pick up beads out of a small container so when I am done working I just put them into pill bottles and pour out what I need next time. I also have a tupperware sandwich container that I keep my odds and end beads in. That way if I am looking for something I check there before I check the store.
Good luck with your idea. I think buying old and rebuilding is a great plan. Might try it myself as well.