I would have guessed that you have to calibrate the detectors relative to each other before trying this. Its also going to be tricky if you use 2 different kinds of ADC for this (c.f. today's delay discussion in the group meeting).
I think Osamu used to look at fast transmission signals by making sure the PD at the end had a 50 Ohm output impedance and just drive the 40m long cable and terminate the receiving end with 50 Ohms. Then both PDs go into the SR785.