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@allObjects
Using the PWM driven pin is there to only 'exercise'/drive your code for figuring timing limits. That is all.
Again, validate some of the wirings and signal behavior and pin mode setup (with pull up/down?) before setting up the watch. The input pins are so sensitive that the wiring capacity is enough to not produce a signal flank when the source is not a push/pull (only an open drain or source).
From what I understand is: about every 4.5ms you get a pulse - interrupt from the acquisition device - that should trigger sending over spi 32 bits to the acquisition device and read 64 bits back from it and then do something with these 64 bits.