dc motor+encoder schema
Oooops!
I doubt about that what I'm going to say is new to you, but if it is only to test something, you could try to use some plastic tubing linking the motor shaft an the home made encoder. Anyway if you plan to use it for more serious work it could be better to eliminate the plastic axis from the mouse wheel, drill it in its center (I guess 2 to 3 mm) and insert in a custom made axis with the 2 to 3 mm external diameter in a end and more in the other end as you can fasten to the motor shaft. That is a very simple lathe work.
It remains the problem of how to align the optical sensors, but I think that you could fix it to the motor frame.
Please let me know what you think.
Best regards.