MarkTheCaz:
Sorry all, the above post was the result of much frustration. In reply to peoples comments I realise the yun is more like a Leonardo
Well, the links to the documentation were made as it clearly states that the AVR part is in fact a Leonardo (using the same chip), so all the differences between Uno (and preceding boards, as well as the Mega(2560)) and a Leonardo do apply.
Before complaining that this and that doesn't work on a Yun, people need first to check that what they are trying to do works on a Leonardo.
On top of that, the basic serial port of the Leonardo part of the Yun is used for the bridge, the communication between the AVR and the MIPS/Linino part. This restriction is also clearly stated in the documentation for the Yun.
As for your problems that the RFID shield only works on certain pins of the Yun, not knowing the exact requirements of that RFID shield, it might be very well down to the differences in the pin layout/capabilities between the Uno and the Leonardo...
Ralf
PS: A nice blog about some of the practical differences (particular pertaining to bad/old habits of Uno/ users) between Uno and Leonardo can be found at Dr. Monk's DIY Electronics Blog: Arduino Leonardo vs. Arduino Uno