Best approach for designing 40A laser diode driver?
This is no easy task to do by simply re-using bits of old motherboards. It's a problem that I feel requires a properly designed solution. I can't imagine that the laser diodes are cheap and because of this I would recommend a properly designed circuit board with a design solution that is tailored for this application. I'm initially thinking of maybe the LTC3882: -



The output parameters can be pretty much controlled from an MCU (Digitally Programmable Voltage, Current Limit, Soft-Start/Stop, Sequencing, Margining, AVP and UV/OV Thresholds) so I thinks it's a solution with high probability of working. Another chip that looks promising is this: -



There are plenty of options from LT - if you use their search engine it narrows down the requirements of 11 to 13 v operation with 1.2 volts and 40 amps output to this web page here.

As for using a micor to control this read what folk are saying about this here: Digital SMPS Vs. Analog SMPS