You were certainly wise to keep such good records, and I am hopeful that Kelloggs/AA will 'do the right thing' and credit those miles -- don't know how they could deny it, actually, with your detailed copies of everything!!
I had an incorrect Kellogg's posting today (not near the magnitude of yours of course!!) and I was impressed with how AA's CSR handled it -- so based on that I am confident that you will receive your miles!!
Biggest question therefore is: what happened to those other milege certs of yours that are missing??!?!? Sounds suspicious unfortunately...