Since appending/combining PDFs with FM Go is not available natively and using a robot machine is not an option, I've dug up a handful of PDF APIs and options. I've got about 1/2 way through the problem, but I am getting some errors with the PDF API and not getting a lot of feedback. If anyone is interested in collaborating, please send a PM. 

Currently, I'm able to send two encoded PDFs from FM to the script and the script will spit back the combined PDF into a container field in FM. Super simple implementation. The PDF that comes back is blank, but has the correct number of pages. The server log shows some errors relating to the PDF API and that's where I'm stuck.

here's some links to the code and questions regarding the issue:
http://stackoverflow.com/questions/34953197/combining-pdfs-with-php-from-encoded-pdfs-error-template-does-not-exist

and 

https://github.com/pauln/tcpdi/issues/3

If anyone has any alternative APIs or solutions, please let me know.

I wanted to followup on this. I did resolve the issue. I uncovered a bug in TCPDI API that was causing the issue. Now, filemaker can successfully POST single base encoded PDFs and then the server will spit back a merged and encoded PDF. Filemaker then re-encodes it and puts it into a container field as the new combined PDF. It's simple, fast, and solved my problem! If anyone is interested, please PM.