You can't use pin 1 or 2 for the software serial RX pin on the Yun. It wouldn't make sense to use pin 1 anyway because this is used for communication with the Atheros module. The only pins you can use for RX are 8, 9, 10, 11, 14 (MISO), 15 (SCK), 16 (MOSI). You can use any pin you like (other than 0 and 1) for the TX pin. Give software serial another try with the correct pins and see if it works.