Great job you've done so far, mrd, my compliments!
My best suggestion for organizing those notes is to use one of the Family History software products available. They'll make organizing those notes so easy, and can crossreference them for you if needed. My personal favorite family history software is Roots Magic because it's proven to be the most versatile and adaptable to your needs. It can also help you put all your information into various reports, as well as make a CD of your work if you wish to share it with other family members. I've tried 4 other programs, but I finally decided Roots Magic made the most sense, especially for a long-term project.
Good luck with the continuance of your project, it sounds like you're well on the road to having a good project going. Again, if there's anything I can do to help you, or check any of my own non-public databases, I'll be happy to help you.
And I'm happy for you in how far you've gotten so far! Good job!