This is a little embarassing, but I don’t think that there was ever anything actually wrong with my JH Living VCO module. I think it was all my error.
I exchanged a few messages with Herr Haible on the electro-music.com forum. He was able to rule out my theory that the substitution of the transistor array was the source of the problem. Once I learned that I went back to basics and checked the value of every component and every solder connectionon the PC board. I completely disassembled the PCB from the panel and tested each oscillator individually, adding connections as I went. I also tested the master section separately. In the end I was able to properly set the 1V/Oct scaling for all three VCOs, with no changes to my original assembly.