First, customize your account so that your transcripts contain only the material you want. Do this on your display preferences page (link below). It sounds like you want to set your display settings to either simplified or traditional and then deselect "show pinyin" and "show translation".http://popupchinese.com/account/customize
Now all you need to do is download everything in bulk. If you use your iTunes feed (delete any existing files and hit the "get all" button) any files you download will have the transcripts formatted according to your latest settings. If you need to change your settings just rinse and repeat.
Incidentally, the transcripts are included as PDF files, but also as id3-tags embedded in the mp3 files themselves. So if you are using an iPhone or iPad it might be enough to simply download the mp3 files and not worry too much about the transcripts.
Hope this helps. Let me know if you run into any problems.