Photointerrupter issue
"Collector current 100 to 400 uA". Across a 1K pullup resistor, that drops 0.1 to 0.4V. 

I would want to drop at least 4V across that resistor - at 100uA it should be 40 kilohms or higher (for the 5mA led current in the datasheet.

You are using a higher LED current than 5ma giving you the higher collector currents (like 700ua) you observe so there may be no need to increase R2 quite so much; 20K may be appropriate.