Robin,
I have viewed your idea several times but I cant get the grip on it. Sorry.
What can we do to solve that (if we can 
)
Do I understand correct that the motor will stop for 0.01 sec?
On facebook I have a video of what the software at the PC side can do although that was with a manual drillstand and encoder strip recorded!.Maybe that gives a better feeling on it.
Do not know if you can view it.
Let me know otherwise I have to search for an other option.