MichaelMeissner:
The other thought if you want to still do IR, is have a second board that only does IR and has a serial/i2c/spi connection to the board running the show. Obviously if you get into multiple boards, you could share some of the PWM support across the boards.
MichaelMesissner beat me too it, but I was going to suggest getting a dedicated IR reciever IC and interfacing with it through a standard digital I/O pin. 
This one is just for decoding signals recieved from IR remote controls, but there are others available for encoding or bi-directional signals.