I would like to receive the “modulated” IR signal into a PWN pin on the Arduino and output it (via serial?) over a cheap NR24 connection to another Arduino where it just outputs that same signal to an IR Emitter using the IR library you mentioned.
Umm, a PWM pin is an output pin (it is turned on/off rapidly to simulate putting out a lower current). Transmitting the IR signal would use a PWM pin to send it, but you don’t use a PWM pin to read it. To read an IR signal, you would need to poll the input (or attach it as an interrupt), and see how long the signal is on and off.
So, if I understand what you are asking, you would have a normal input that sees the pulses, and using the library it figures out what is being pressed. Presumably you would then write a character or more on the serial line to the other Arduino, which in turn generates the signal. There is likely some small delay for the encoding and decoding. I imagine if the distance isn’t too large, it might be simpler to eliminate the second Arduino, and just run a long wire from the sensor. It depends on the distance and the electrical noise in the area. Another thought would be to run a fiber optic cable carrying the IR signal, instead of a sensor on an electrical wire.
If you only have two different buttons that are being pressed, you can use this chip from Sparkfun. According to the documentation, you can program it with two different signals, and it will raise two different input signals, depending on which button was pressed. This saves you from having to have the Arduino trying to decode the signal, and the chip does it in the background: https://www.sparkfun.com/products/8753
The Simrec SIS-7C is the big brother chip, where it allows you to recognize 7 different IR buttons: http://www.simerec.com/chips.html
If the control you are trying to read uses the NEC protocol, this chip would be similar to the SIS-7C: http://www.ebay.com/itm/350608682887?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1439.l2649