ok, i finally figured out where the discrepancies were. first, for some reason 2-4 books didn't download. it's possible i missed them because amazon only allows 10 at a time and removes your checkmarks so you have to keep a mental note of where you were.
but the weird part was that i kept seeing a kindle users guide and a 2nd edition of it. but they didn't show up consistently and i didn't think they were included in the amazon count when showing the /books/ category. but i finally hit upon the /dictionary/ category and there were no less than 5 copies of the guides in there. i (ass)ume that every time i bought a kindle amazon added one automatically in that category. but there were no copies on my kindle.
anyway, i simply deleted them from amazon and it confirmed that amazon wasn't including them in the 56 count. very confusing and i'm glad i figured this out before i put back over 2500 of my calibre books.
at least now the numbers are matching, i have 56 books showing on amazon and 56 showing up in the /Amazon/ collection i created. the reason i had to create this category is that otherwise i won't know which books came from an amazon download and which from a calibre sideload. well, i could figure it out from calibre of course.
many thanks for the helpful tips--they got me there eventually and my ocd soul thanks you as well.
/guy