The case price really isn't bad. But you may not need so many. I was lucky in that mine were given to me by the museum. They don't do stuff like that anymore though.....Ouch they are expensive...
You can probably find them at collector's/memorabilia stores. They look like those cases people display signed footballs and stuff in. In fact, if you run a google image search for "Beanie Baby Box" those look similar and they do come in different sizes. I don't know what part of California you are located, but Frank & Son would definitely have them (http://www.frankandsonshow.net/).I tried looking for those mesh lids at home depot and lowes but they only come with sink aerators. It is seriously annoying that I can't find the little things that I need haha. I'm also looking for these acrylic containers with the deep lids, but the dollar stores and Wal-mart doesnt carry them. I'm surprised that Hobby Lobby doesn't even carry any. I found a couple but the don't have the deep lids like I want. I don't mind buying them online but I'd rather just go to the store and get them conveniently. If anyone can find where I can get these please let me know.