what sensors are You using? I suppose You are using
photo-detector with embedded L-F converter + color glass filter.

I think You must see other variants - http://www.keyence.com for exmple.
Chip 3-color sensor / analog output (see hamamatsu.com for example) will need 3 channel ADC or L-F converters, but will
use one optic path. Even with one ADC and multiplexing You can
make 1..3 msec for object analizing (homogenous colored object,good lighting and black screen).
Your default scan time is much more than 8 msec -> 8msec + 114msec for travel time (48/420=118 msec). When You acqiure last channel(B) for first object , another 6 objects are between first and last sensor (48 mm / (4mm+4mm))....
Data from R,G and B is comming at different time, so You cannot
read simultaneously.
In Your default system You must have
at least 7 counters( 7 objects in same time between R and B sensors, and some objects between trigger and 1-st sensor) driven by timer and started by trigger.