Once i did use UART signals over cheap RF modules and it worked no problem as long as the baud rate was kept low enough. The modules ware rated for 2400bps only anyway. UART worked at that speed but about every 50th character was corrupt but using a lower speed it worked no problem. But i cant be positive if it works like that for IR too since i havent tryed that.
As I understand it, RS-232 comms (serial communications) needs tight timing, controlled by a clock signal, to work right. Going over an IR or RF link, there is no common clock signal and this messes up the timing. Therefore, other encoding schemes are used instead.
You could also try 40KHz transducers, put the RX on the one board and TX on the other. You will need an op-amp circuit on the reciever side, but that will also help to set the sensitivity.