One word - Goodreader. Look for it in the app store. I think it's $5 or somewhere around there. Buy it and you can fix this problem.
iBooks on the iPad, where pdf files get saved by default, is terrible with this. You can't rename files and you can't sort anything.
Goodreader has a Document Manager built into it. You can easily open the Document Manager, rename files and then re-save them with the new name. They will then sort by the file name you give it. Easy. I use it all the time on my iPad. You can use Goodreader to open pdf files, txt files, doc files and a lot of other formats, too. They call it the "Swiss Army Knife" of file management apps for the iPad.