Nice to see your advice/ideas/concerns.
First, I never planned to  find a sensor that output Amiga compatible signals. I can program Atmel  AVR's so that's not a problem. I just have to learn how to read the  data from the sensor and then convert it to Amiga format. If fact, I  have a couple of spare ATtiny2313 with should be useable in a prototype. I probably could find a smaller one that is more production friendly.
I  bought a cheap mouse online and I will gut it and see if I can use the  sensor, lens and LED. What worries me a bit is the space inside the  mouse case. But with the ball out of the way there will hopefully be  enough space to mount the sensor/lens without having to damage the mouse  case. 
A new PCB has to be designed. I guess I can use a protype  board to begin with. I haven't designed a PCB for many years but I  guess it's like riding a bike...
Yes, I could get a proper  optical mouse and a signal converter if I wanted, but I like the  challenge. I became and engineer because I like to build and develop  stuff. The end use is secondary.