Like you, I'm a big fan of ziploc bags for storage. Like GG, I don't put needle tips in the bags unless it's a WIP.
Stash goes in the ziploc, then into a plastic bin, and is logged into my Ravelry stash so that I know what I have, and where. I'm in the process of assigning kit stash to projects so that I don't unwittingly use kit stash for something else.
Oy! Cataloging THAT for the first time was a nightmare! And if my bins are full, I don't buy more yarn and work out of stash. Trying to keep my house from turning into a one woman LYS has become real work.
But it's a labor of love.
Your idea of storing as kits is a great one!