yeah, that is a real strange power supply arrangement. A test for transistor circuit analysis.
To make it easy for me and others to follow when you state your measurements, you should indicate where you are taking them, like saying, reading taken at Q16,base(D4 cathode) instead of "A reading of 39v instead of 32v at the second voltage spot"
If that is this place, then the 32V zener(d4) seems to be acting up, replace it with
771-BZX79-C30133
Little hard to read my schematic, so you changed C67(220uF/50V)?
Also check those 1.2K ohm resistors,R100,R?
Q17 acts a shunt regulator with it bias set by the negative voltage doubler made up with C64,D3,C63. It certainly would help if they printed more voltages on the schematic, what would it have taken them to do this, nothing, bunch of fools.
Good luck
Rick