Hi Aether,
I haven't had a good look at this yet but I will read up on everything over lunch and try to get back to you. Like you, I am an Arduino tinkerer; my current project is timing & start light displays for my local RC car club.
Two things spring to mind before I read up:
1) Have you considered the ATTiny 45/85 ICs? Think of them as tiny Arduinos, they're only 8 pins in DIP/DIL packaging. About the same size as a fingernail. It would be very easy to design a custom PCB for one of these and a IR LED. Whether they're the right IC for you depends on what code you use in your Arduino sketch as they have a limited instruction set.
2) Depending on how well your IR send/receive is working, an alternative library to consider is the
IR Remote library.
When I've finished my timing board project, I'm planning on making an IR LED-based personal lap counter, so I'm very interested in helping in whatever way I can.
P.S.
This switching regulator would be a good way to power your transponder from the car (2S?) battery.
Best of luck!
Joe