[AVR32] fix serial port setup on ATSTK1000

Fixes to USART setup on the stk-1000 ... don't configure USART 2, since
its TXD/RXD are used for INT-A and INT-B buttons; and configure USART 0
(for IRDA, and with corrected IRQ) iff SW2 has a non-default setting.

Signed-off-by: David Brownell <dbrownell@users.sourceforge.net>
Signed-off-by: Haavard Skinnemoen <hskinnemoen@atmel.com>