How to determine the center frequency of a photodiode?
The peak sensitivity wavelength of the photodiodes is completely unrelated to the PWM frequency that might be used to modulate the IR signal. The system you have assembled does not use modulated IR and cannot benefit from applying PWM to the emitters.

What you can do is verify that the peak emission from your IR LEDs is close to the wavelength of peak sensitivity for the photodiodes. You could also consider using an IR filter that would block visible light from getting to your photodiodes. They may not be very sensitive to visible light but there is a lot of visible light that competes with your IR signal.