Gravis.. good point.. Actually something like this is already done.. When the command is run, the script prints out how far the cylinder lenses and lasers are away from the "optimal" position. This is not done for the photo-diode and mirror, here you r suppose to do it visually.

On my current desktop, I can only use windows. It wasn't easy to install pyOptools so that's why I used LXQt as it is so minimal.. It is quite nice indeed :-).

Very cool.  I don't know enough about optics to grasp all of this but since no assembled device is exactly like the design, consider writing a script that would slightly move optics related components out of place/askew and test to find the limits of what will produce an acceptable output.  This could be done mathematically so if that's your strong suit then go with it.  It would be useful since the limits identified can then be factored into the design if you find a component that is especially sensitive to error.  One last thing, the LXQt desktop is a good choice. :)