Hello,
what do you mean with "fix the PDF file"?
Seems a firefox bug to me. Try to open the PDF file with Google Chrome, In firefox there are problems loading the correct font but in Chrome there are no problems.
Maybe I misunderstood your project description, sorry for that.
By the way, if you want, send me a private message so that we can discuss about this.
I've been using Ubuntu (Linux) for years, and I'm an expert Java developer so, probably, I can help you.
Looking forward to chatting more,
Domenico