Just went through this process on a gearbox that hadn't been touched. Sure enough, goop/sludge. I have to admit, I wasn't thinking about the opto interrupter at all during the process, and installed it the way it was when I took it apart. As far as I can tell, the trunk is aligned properly.
As I did this, I noticed the cable connecting the motor and motor control board was soldered on, so I took the time to replace with quick disconnects on the motor side and a molex connector on the board side.
After cleaning/de-carbing the gearbox and superlubing it, it definitely runs faster and quiet. Here are a photo of the inside of the dirty gearbox for your disgusting pleasure.