I decided to take apart the AF module from the 550EX flash mainly to see if I could use my own LED in the AF module lens.
The unit is comprised of a lens and holder assembly, and an LED assembly. The LED assembly has the LED (which I believe to be a near IR LED) glued to the back of a lens.
The pattern the AF assist module projects is created right on the LED itself, unlike the 540EZ module. The pattern created by the 540EZ module is drawn on a small piece of plastic that lives inside the module. On the 5503EX module, the pattern is right on the LED.
So it looks like there’s no replacing the LED in this module.