I've been using PDF::API2 for some time, but for PDF creation, not modification. The author is constantly working on it, and there is an active message board where some quite knowledgable people are eager to help out. I found a couple of message like this one which talk of modifying the streams directly.. some working with Text::PDF instead of PDF::API2.

I don't know much about PDF streams myself, and haven't had to modify existing PDF's, but this module and the people working on/with it can probably give you some useful guidance.

Good luck,
-=rev=-