What I have done is scan them all at the highest possible resolution, both sides of each sheet. Then store each one in individual archival folders then put into a safety deposit box.

I have documents that are nothing more than handwritten notes puton a piece of scrap paper in the late 1800s which would've otherwise been tossed away but, to me, are precious.

You should absolutely preserve those documents. They sound extremely fascinating. If you're interested in making them accessible to historians, I'd suggest contacting your local historical society, or perhaps the Japanese American National Museum (http://www.janm.org/) and discuss donating them. Whatever you do, please, for the love of God, preserve those documents.