Alignment steps are documented in Prodigy's Technical Service Manual. When doing the temperature adjustment of OSC1 and OSC2 I found David Morrins instructions very valuable. When adjusting the temperature trimmer I always checked that the voltage at pin 7 of U2/U4 was negative. If this voltage jumps to positive voltage then the heater circuit is saturated and will not track temperature. If this happens turn the R14/R35 trimmer to other direction so that you get the pin 7 back to negative region.
Original Prodigy's OSC1 is tuned lower (32-16-8) than OSC2 (16-8-4). This is not necessary if you are using the external keyboard-input that doesn't have the 2.5 octave limitation of Prodigy's keyboard. I tuned the OSC2 similarly to OSC1.