I have used that chip for a project a while back. I also found setting it up to be slightly frustrating, because at th beginning, it would simply not respond at all. The datasheet is long and not too accessible unfortunately, which means, read it 3 times and pay attention to all the details.
The most time consuming issues I encountered, if I remember correctly, where getting the framing right (you need to put the commands you send into checksummed frames... and this is mentioned in a whole different section of the documentation), and getting the timing right (if you poll the chip too often, it'll hang.) Never fully understood what's required for a reliable reset sequence either. At some point I hit a timing that seemed to work for resets and decided to just not touch that part anymore

I was using I2C at the time though, not the serial port. I have some Arduino code somewhere that communicates with the PN532. If you feel that it might be useful to you, I'll see whether i can dig it up.