Any ideas to make IR LEDs identifiable during position-tracking?
You forgot some sort of initialization/broadcast heartbeat, otherwise the marker would not know when to light up. Depending how good your sensors and leds are, you may be able to use different slices of the IR spectrum. This way you could distinguish an LED with a 300 µm wavelength from one with 200 µm. If you have multiple cameras, you could use different optics/filters (is feasible).
Otherwise invest in a camera with a higher frame rate and let each marker blink in an unique pattern. The pattern must not only be on/off, but can leverage frequency modulation too.