I am not sure if I follow - is the difference due to the fact that due to delay between IRQ and readout of the second sensor it has been either covered or opened?
Anyway, it is not possible this way...
For this to work tension must be applied to the chain around the place the sensor is located (otherwise sagging of the chain will confuse the sensor). The problem is that with the forward movement the tension is on the lower part of the chain and with the backward movement on the top part... Of course, this in itself could be an indication of the direction of movement, now just to couple it with the speed reading...
Oh: the sprocket! The wheel itself is free, but the sprocket is not! No problem with the tension, either.
I guess I will have to sleep it over!
P.S. One more thing I forgot to mention - the advantage of hooking the mouse wheel to the chain (or, rather a small sprocket attached to it) instead of the main wheel is that the gear ratio is much more palatable... The sprocket I've got is somewhat smaller than the bike sprocket (did not get around to count the teeth), but not below 1:2 - the wheel speed is typically around 4 rotations per second, so I guess it should work out OK.