Transponder mounting examples
Using a small rectangular section of lexan, folded and double sided taped to a side window a mount can be created. Ream a small 4.8mm hole in the lexan and fit the LED before each run.
Chassis Mounted
Using an areial tube and short length of heat shrink a very neat solution can be created to hold the IR LED at the correct height and with very little movement while the car is in motion.
This can also be done with a piece of lexan. The example shown below is a section of lexan taken from a wing. The curved section reduces the flexing.
Chassis mounted on tube 
Chassis mounted on lean 
Window Mounted