If you open up the .twb file in notepad++, you'll see it's nothing more than XML. You should also note that for the fields you've already renamed, you'll see something like
caption='Your Friendly Field Name'
While editing the .twb file manually is unsupported, I can tell you're technical enough to handle it on your own.
You can use some sort or regex expression to ADD the caption attribute where it is missing, and plug in the friendly caption value you want.
Thanks a lot Russell - that is a wonderful tip to know for those times that I really need to venture into mass renaming by hacking into the TWB file.