Hi Oso M,
The pinout across the serial port is the same order as on the FTDI cables and 3DR radios. Their wiki has some nice pictures of a connection which is the same as the RFD900 across the serial port. http://code.google.com/p/ardupilot-mega/wiki/3DRadio
I will make a few good diagrams showing the connection to APM1/2 shortly.