Not directly related to your question, but concerning transmitting of an IR signal; here's my experience. I had in the past tried pretty much what you are doing (hardware PWM on one pin, and the data on another). I then modified the code to control the PWM itself as per the data bits, and got a much better sinal (in terms of shape and amplitude). So much so that I could even get rid of the transistor, and drive the LED directly (in series with a resistor) from the pin. Additional bonus being saved an IO pin as well.
Regards,
Anand Dhuru
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