In addition to a missing input filter, there's a couple of other issues that you need to consider. You mentioned that inDesign didn't have compression. I don't know about that, but Compress::Zlib v1.0 is a prerequisite for PDF::API2. As for encoding, PDF::API2 uses Encode and utf8. utf8 is default; hence, you don't need to use  -encoding => 'utf8'. I tried it, and it spit it back at me. Also, I had some problems getting the fonts to work. You might want to check out the examples for truefonts and corefonts.